Chapter 5:
	A Protein Motions Database
	Mark Gerstein
	Department of Structural Biology
	Stanford University, Stanford, CA 94305
	mbg@hyper.stanford.edu

Introduction
	This chapter will present a computer database containing a listing of protein motions. It is arranged around a 3-level classification scheme for protein motions and includes domain motions, loop motions, and subunit motions. In addition to listing the relevant proteins and descriptions of their motion, the database contains pictures of the motion and hypertext links to journal articles and molecular coordinates. It is accessible over the Internet using the World Wide Web 1 with the following resource locator (URL):* 
http://hyper.stanford.edu/~mbg/ProtMotDB/.
	As shown in figure 5.1, using the database is very easy.  You access its main page with one of the popular World-Wide-Web browsers such as Mosaic or Netscape. You can type various keywords into this page, and the database will display the entries for the relevant protein motions. Finally, you can click on various highlighted words in these entries, and this, in turn, will either link you directly to a relevant Medline abstract from the journal literature or bring up pictures and plausible movies showing the protein motion. 
	The protein motions database should be a great use to the community of structural biologists because it collects in one place many different motions, helping with comparative analysis. This is particularly relevant at present because of the large and exponentially increasing number of solved protein structures (currently estimated at 3000, increasing by about 1 a day 2). Furthermore, the graphical and interactive nature of the database is particularly well-suited for the understanding of protein motions, which are often difficult to represent on a static printed page. This is particularly true because many published papers about interesting protein motions do not precisely describe the relationship between the motion and specific publically accessible coordinate files and viewing orientations. (That is, many papers do not tell you that, say, the atomic coordinates for the open form have identifier 6LDH and those for the closed form, 1LDM and that the motion is best viewed when looking down the crystallographic three-fold after fitting residues 5 to 90.)
Which proteins are in the database and how they are organized?
	The database attempts to cover all instances of protein motion for which there is at least some structural information — i.e. at least one conformation has been solved by crystallography or NMR spectroscopy. The classification scheme is an expanded version of the one described in Gerstein et al. 3 The basic division is among three categories:
(A)	domain motions;
(B)	motions smaller than domain motions, e.g. loop motions; and
(C)	motions larger than domain motions, i.e. subunit motions.
Motions smaller than domain motions include loop closures, such as the one in triose phosphate isomerase, and motions of secondary structures, like the sliding helices in insulin. Each of these three basic categories is then subdivided into two sub-groups:
(1)	proteins for which two conformations (i.e. open and closed) are known from crystallography or NMR (nuclear magnetic resonance), and 
(2)	proteins for which only a single conformation (i.e. open) is known but for which there is compelling evidence for motion. 
Often this evidence for motion is similarity to a protein in the first group. That is, the heat shock protein has only been solved in one conformation but because of its structural similarity to hexokinase 4, we suspect it undergoes a similar domain movement. Finally, for the motions of domains and smaller units (categories A and B) each of the two sub-groups is further subdivided depending on whether the motion mostly has a hinge or shear mechanism:
(i)	motion predominantly involves localized hinges
(ii)	motion predominantly involves sliding shear motions, not hinges;
(iii)	motion can not yet be classified; and 
(iv)	a special case motion that is clearly neither hinge nor shear.
(v)	motion that involves a partial refolding of the protein
Hinge and shear motions are described in detail in Gerstein et al. 3 and in chapter  4. Refolding includes motions such as those found in the serpins and in hemaglutinin. For the motions of subunits (category C), each of the two groups is differently subdivided depending on whether the motion is (i) allosteric (as is the case with hemoglobin) or (ii) non-allosteric. 
	The overall classification scheme is shown in figure 5.2. The numbers associated with the three levels in this scheme provide a simple classification descriptor for each protein motion. That is, giving the classification number [A.1.i.] to the protein lactoferrin says that it has a hinged domain motion, for which both open and closed conformations are known. Some proteins can be classified in a number of different ways in this system because they undergo more than one motion. Sometimes these different motions are independent, as is the case with the immunoglobulins  (see chapter 7), and the protein deserves to be classified in multiple categories. However, often they are not. A larger motion can drive a smaller motion, such as a domain motion having many associated loop rearrangments, and in this case the protein is only classified in terms of the larger movement. 
What information is associated with each protein in the database?
	The information associated with each protein is described in detail in the appendix. The database itself is stored as a number of fields in a tab-delimited text file. This simple format allows it to be easily processed by a variety of different programs, from PERL scripts (common on Unix platforms) to Macintosh mail-merge programs. The database is designed so it will be possible to automatically add more entries as long as they follow the submission format described in the appendix. 
	Originally, the information associated with each protein was basic: the classification number described in the previous section, a brief text description of the motion, the Protein Databank (PDB) 5 identifiers of the conformations (if available), and the references to the papers describing the motions. As the database project has progressed more and more information has been added to each entry. Some entries, for instance, now have links to simple pictures and even movies (in MPEG format). The PDB identifiers associated with each entry have been made into hypertext links directly to the structure entries at Brookhaven, to sequence and journal cross-references via the National Center for Biotechnology Information’s (NCBI) Entrez database 6, and to a listing of related structures via SCOP. 7 Some of the references have also been directly linked to Medline abstracts, again via Entrez. The transformations and residue selections needed to optimally superimpose and orient each coordinate set to best see the motion can also be associated with each entry. 
Plans for the future
	The goal for the future is to have a larger more comprehensive database that is continually kept up-to-date. To achieve this, it will be essential to have automated submission of entries (using such a form as that shown in figure 5.1) and to use simple computer programs to fill in automatically and objectively many of the fields associated with each entry. In theory, given the PDB identifiers of two conformations, one should be able to immediately connect via a network searching tool, such as Entrez, to all the the relevant literature and the coordinates. Then one could use automatic sieve-fitting and hinge detection procedures on the coordinates 8, 9 to optimally superimpose the non-moving parts of the structure. This would allow automatic characterization of the magnitude of the motion and whether it involved a domain, loop, and so forth. A screw-transformation 10 could then be used to re-express the motion in such a way that the translation is minimized (see chapter 4). This would give a good orientation to view the rotation, and if the new translation were small and the new rotation axis passed through a portion of the polypeptide chain, the motion could be automatically identified as a hinge; otherwise, it would be shear. Finally, one could use the superposed and reorientated coordinates to automatically generate some useful pictures. Movies could even by generated “on the fly” by doing torsion-angle interpolation in any putative hinge regions to generate intermediate conformations (B. Park, personal communication). Alternatively, the database could be coupled to an interactive 3D-viewer such as RasMol 11 or Kinemage 12 and the superposed coordinates could be viewed from any orientation. 
	Thus, given two PDB identifiers one should in principle be able to automatically describe much of the motion, construct hypertext links to other databases, and draw useful pictures. 
Acknowledgements
MG received support from a Damon Runyon-Walter Winchell Fellowship (DRG-1272).  

References
1.	Schatz, BR,  Hardin, JB. NCSA Mosaic and the World Wide Web: Global Hypermedia Protocols for the Internet. Science 1994; 265: 895-901. 
2.	Orengo, CA. Classification of protein folds. Curr Opin Struc Biol 1994; 4: 429-440. 
3.	Gerstein, M, et al. Structural Mechanisms for Domain Movements. Biochemistry 1994; 33: 6739-6749. URL: ftp://hyper.stanford.edu/pub/mbg/DomainClosure/.
4.	Flaherty, KM, et al. Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70-kDa heat shock cognate protein. Proc Natl Acad Sci USA 1991; 88: 5041-5045. 
5.	Bernstein, FC, et al. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977; 112: 535-542. PDB URL: http://www.pdb.bnl.gov.
6.	Epstein, JA, et al. WWW Entrez: A Hypertext Retrieval Tool for Molecular Biology. 2nd Ann Int WWW Conf 1994; (in press). http://atlas.nlm.nih.gov:5700/WWW2_paper2.html.
7.	Murzin, A, et al. SCOP: Structural Classification of Proteins. J Mol Biol 1995; 247: 536-540. URL: http://prosci.biomol.uci.edu/scop/.
8.	Gerstein, M,  Chothia, CH. Analysis of Protein Loop Closure: Two Types of Hinges Produce One Motion in Lactate Dehydrogenase. J Mol Biol 1991; 220: 133-149. 
9.	Huang, E, et al. Automatic and accurate method for analysis of proteins that undergo hinge-mediated domain and loop movements. Curr Biol 1994; 3: 740-748. 
10.	Gerstein, M, et al. Domain Closure in Lactoferrin: Two  Hinges produce a See-saw Motion between Alternative Close-Packed Interfaces. J Mol Biol 1993; 234: 357-372. URL ftp://hyper.stanford.edu/pub/mbg/Lactoferrin.
11.	Sayle, R. RasMol. 1994; ftp://ftp.dcs.ed.ac.uk/rasmol.
12.	Richardson, DC,  Richardson, JS. The kinemage: A tool for scientific communication. Prot Sci 1992; 1: 3-9. Journal URL: http://protsci.biomol.uci.edu/.
13.	Brenner, SE,  Hubbard, TJP 1995. A specification for defining and annotating regions of macromolecular structures. In: Rawlings, C, et al., ed. Proc. 3rd Int Conf Intell Sys Mol Biol. Menlo Park: AAAI Press, 1995. http://www.bio.cam.ac.uk/annmm/.

Figure 5.1	What the database looks like on the screen
Part A shows a picture of the main hypertext page to the database. One can type keywords in the small box at the top. Part B shows an entry retrieved by such a keyword search. A click on highlighted words in this entry will bring up a graphic (which is shown in part C). There is a special form for submitting entries to the database (shown in part D). 

Figure 5.2	Schematic showing overall database classification scheme

Appendix 5.1	Detailed contents of a database entry
What follows is a description of the submission format to the database. The description follows a simple Backus-Naur form (BNF) style grammer.  A few preliminary comments:  <something>... means that one or more instances of something can be specified, and[<something>] means that something is optional. Most of the records consist of <Free-Text> which is a sequence of normal printing ASCII characters, except for the ‘@’. Whitespace, including returns, is ignored in parsing an entry. Each entry in the database has the following form:

<Entry> := @ENTRY-START   <Name-Text> 
             @CLASS       <Class-Num> [<Class-Text>]
             <Description>
             <Structure>...
             <Reference>...
             <Graphic>...           
           @END-ENTRY
<Name-Text> is the <Free-Text> name of the protein. <Class-Num> and <Class-Text> are taken from one of the following table:

<Class-Num>  <Class-Text>
-----------  ------------
A.1.i.       Known Domain Motion, Shear Mechanism 
A.1.ii.      Known Domain Motion, Hinge Mechanism 
A.1.iii.     Known Domain Motion, Unclassifiable Mechanism
A.1.iv.      Known Domain Motion, Special Mechanism, Neither Hinge nor Shear
A.1.v.       Known Domain Motion, Partial Refolding of Structure
A.2.i.       Suspected Domain Motion, Shear Mechanism
A.2.ii.      Suspected Domain Motion, Hinge Mechanism 
A.2.iii.     Suspected Domain Motion, Unclassifiable Mechanism
B.1.i.       Known Fragment Motion, Shear Mechanism 
B.1.ii.      Known Fragment Motion, Hinge Mechanism  
A.1.iv.      Known Fragment Motion, Special Mechanism, Neither Hinge nor Shear
B.1.iii.     Known Fragment Motion, Unclassifiable 
B.1.v.       Known Fragment Motion, Partial Refolding of Structure
B.2.i.       Suspected Fragment Motion, Shear Mechanism 
B.2.ii.      Suspected Fragment Motion, Hinge Mechanism 
B.2.iii.     Suspected Fragment Motion, Unclassifiable 
C.1.i.       Known Subunit Motion, Involving Allostery
C.1.ii.      Known Subunit Motion, Not Involving Allostery
C.2.i.       Suspected Subunit Motion, Involving Allostery
C.2.ii.      Suspected Subunit Motion, Not Involving Allostery
    
<Description> := @DESCRIP-START <Free-Text> @DESCRIP-END
The description record contains such things as the total rotation in degrees, how many hinges there are in total, does the motion involve binding to ligand, and so forth.  
            
<Reference> := @REF [@MED <Medline-Number>] [@INT <Internal-Pointer-Number>] 
The <Medline-Number> is the Medline Unique Identifer Accession Number, which is an integer number like 94157914. <Internal-Pointer-Number> is the number of the reference in external bibliography file (usually for references that are not accessible via medline). All these external references are stored in either Medline Medlars export format or in EndNote. 

<Structure> :=  @PDB-START         <1pdb>
                   [ @STATE        open | closed | halfway               ]
                   [ @TRANSFORM    <rotation-matrix> <translation-vector>]
                   [ @SELECT-FIT   <residue-range-selection>...          ]
                   [ @SELECT-SHOW  <residue-range-selection>...          ]
                   [ @SELECT-HINGE <residue-range-selection>...          ]
                @PDB-END
<1pdb> is the normal four character Protein Databank identifier, <rotation-matrix> is just the nine real numbers in a rotatation matrix expressed in the following order: r11 r12 r13 r21 … <translation-vector> is the three real numbers in a translation vector: tx, ty, tz. The rotation is applied before the translation, so the overall transformation has the following form:
	
where the unprimed coordinates (x, y, z) are taken from the PDB file and the primed coordinates have been moved into an orientation so that all the structures superpose and are arranged optimally to view along the z’ axis. 

<residue-range-selection> := <one-residue-selection> .. <one-residue-selection>
<one-residue-selection>   := <residue-number>[:<chain-identifier>]
The <residue-number> and <chain-identifier> are as in the PDB file,  so a sample <residue-range-selection> are 23:A .. 25:A or 24 .. 24. In the future, the Annmm standard 13 may be a more rigorous and comprehensive way to encapsulate the information in each structure record. 

<Graphic> := @GRAPHIC-START <URL>
                [ @TYPE  gif | mpeg | ps                           ]
                [ @CREDIT <Free-Text>                              ]
             @GRAPHIC-END
<URL> is a World-wide-web Uniform Resource Locator, describing where to find the picture. This can be reduced into just a filename. The text associated with @CREDIT  describes the graphic and gives appropriate credit to whoever drew it. 

Appendix 5.2	What version 1.5 (April 1995) of the database contains?

A	Domain Motions
1	Proteins for which open and closed conformations are known 
i	Motion is predominantly shear
•	Citrate Synthase.  [1CTS, 3CTS] Shear motions at many helix-helix interfaces shift mainchain atoms up to 10 A. Citrate synthase is one of the clearest examples of a domain closure occurring through shear motions. The molecule is a dimer, and each monomer comprises a large domain, containing 15 helices, and a small domain, containing 5 helices, with the active  site cleft between them. The domain closure involves the small domain closing over the large one, burying the substrates in the active site. An extensive interface between the large and small domains prevents closure taking place through a hinge mechanism. Closure is produced by the summation of many small shear motions between pairs of packed helices. The overall motion results in a helix on the far side of the small domain shifting by 10 A and rotating by 28 degrees, thereby moving an adjacent  loop over the active site. Each local shear motion involves one helix moving relative to another by main-chain rotations and shifts of up to 13 degrees and 1.8 Å. To a good approximation, the main chain of each helix moves without deformation as a rigid  body. The shear motions are facilitated by small deformations in the loops linking the helices. J Mol Biol 158: 111-152.  J Mol Biol 174: 175-91. 
•	Aspartate Amino Transferase (AAT).  [9AAT, 1AMA] Shear motion at 2 interfaces combined with hinge in a kinked helix. The domain motion is mainly the result of just two shear motions, which occur in perpendicular directions. AAT has an active site situated between a large and a small domain, and on substrate binding the small domain closes over the active site. The major shear motion involves a 13 degree rotation of the the small domain relative to the large one. A secondary shear motion moves a helix on one side of the small domain in a direction perpendicular to both the interdomain interface and the direction of the  of the other shear motion. With a 1.2 Å shift and a 10 degree rotation, it 'drops down' to cover the active site. The shear motions in AAT are facilitated by a hinge motion in a long interdomain helix. This helix is kinked by 17 degrees in the open form  and changes its kink angle by 12 degrees on closure.  J Mol Biol 225: 495-517.  [92395661]
•	Trp Repressor (TrpR).  [1WRP, 2WRP, 3WRP] Shear motion between 2 helices adjusts position of helix-turn-helix reading head domain to enable it to bind DNA. The trp repressor is a small protein that regulates three operons involved in the synthesis of tryptophan. It is a dimer, and each subunit contains six helices, divided between two domains. The central core of the molecule is formed from four helices from each subunit. On either side of this core, helix-turn-helix motifs form two symmetrically arranged DNA 'reading head' domains. Between the central core and the reading-head domains, there are two binding sites for L-tryptophan, which need to be filled for trp repressor to recognize DNA. Comparison of the holo and apo forms of the repressor shows that the binding of L-tryptophan shifts alpha carbons in the reading head domain by up to 4 Å. These shifts are produced by separate shear motions of the two helices in the reading-head domain (0.75 to1.5 Å, 5 to 20 degrees). These helix motions move the reading-head domains further apart than they are in the apo form so they are correctly separated to bind DNA.  Proteins 3: 18-31. 
•	Hexokinase.  [2YHX, 1HKG] Shear motion with XBAaba layering and prominent crossed helices at interdomain interface: Hexokinase has 3 moving layers in one domain that shift relative to 3 rigid layers in the other domain. This distinctive layering pattern is of the form XBAabx, where abx are the 3 moving layers and XBA the rigid layers. The interface between the two  middle layers is where the major shear motion occurs. One layer of helices from the mobile domain (a) slides over a layer of helices from the motionless domain (A). Helices in these two layers, which in a sense form gears upon which the domains slide, are often 'crossed'. Near to the a and A layer helices, the ligand binds in the interdomain cleft . Packed onto either side of the central layers of helices (a and A) are sheets (b and B) from the mobile and motionless domains, respectively. The mobile sheet  (b) forms a second moving layer, which slides over the helices, and packed onto the other face of this sheet is a third layer (x) which moves with the sheet. Symmetrical to this third moving layer (x), a third motionless layer (X) is packed onto one side  of the static sheet (B). In hexokinase layer x and X are made up of helices. Proc Natl Acad Sci USA 75: 4848-4852.  J Mol Biol 174: 175-91.  J Mol Biol 140: 211-230. 
•	Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH).  [1GD1, 2GD1] Shear motion with XBAaba layering. GAPDH has 3 moving layers in one domain that shift relative to 3 rigid layers in the other domain. This distinctive layering pattern is of the form XBAabx, where abx are the 3 moving layers and XBA the rigid layers. The interface between the two middle layers is where the major shear motion occurs. One layer of helices from the mobile domain (a) slides over a layer of helices from the motionless domain (A). Helices in these two layers, which in a sense form gears upon which the domains slide, are often 'crossed'. Near to the a and A layer helices, the ligand binds in the interdomain cleft . Packed onto either side of the central layers of helices (a and A) are sheets (b and B) from the mobile and motionless domains, respectively. The mobile sheet  (b) forms a second moving layer, which slides over the helices, and packed onto the other face of this sheet is a third layer (x) which moves with the sheet. Symmetrical to this third moving layer (x), a third motionless layer (X) is packed onto one side  of the static sheet (B). In GAPDH layer x is made up of helices and layer X is a sheet from another subunit. J Mol Biol 203: 1097-1118. 
•	Alcohol Dehydrogenase (ADH).  [8ADH, 6ADH] Shear motion with XBAaba layering: ADH enzyme has 3 moving layers in one domain that shift relative to 3 rigid layers in the other domain. This distinctive layering pattern is of the form XBAabx, where abx are the 3 moving layers and XBA the rigid layers. The interface between the two middle layers is where the major shear motion occurs. One layer of helices from the mobile domain (a) slides over a layer of helices from the motionless domain (A). Helices in these two layers, which in a sense form gears upon which the domains slide, are often 'crossed'. Near to the a and A layer helices, the ligand binds in the interdomain cleft . Packed onto either side of the central layers of helices (a and A) are sheets (b and B) from the mobile and motionless domains, respectively. The mobile sheet  (b) forms a second moving layer, which slides over the helices, and packed onto the other face of this sheet is a third layer (x) which moves with the sheet. Symmetrical to this third moving layer (x), a third motionless layer (X) is packed onto one side  of the static sheet (B). In ADH layer x is made up of helices and a sheet, and layer X is made up of helices. In addition to its shear motion, ADH also has two well defined hinge points.  J Mol Biol 146: 561-587.  J Biol Chem 261: 15273-15280. 
•	Endothiapepsin.  [4APE, 5ER2] Small shearing motion at 1 interface between domains (17 degree rotation and 1 Angstrom displacement). EMBO J 8: 2179-2188.  [90005421] Proteins: Struc Func Genet 12: 158-170.  [92294166]
•	Phosphofructokinase (PFK) (not allosteric transition).  [1PFK] Each PFK subunit consists of two domains. Comparison of the 2 R-state subunits in the asymmetric unit, shows that one is more closed than other. This small domain closure shifts CA atoms up to 3.5 A and involves and overall rotation of 5.5 degrees and an overall translation of 0.45 A. Despite the identification of a clear rotation axis, the motion is best described as proceeding through a shear mechanism. Three helices (2, 4, and 5) on the outer layer of the protein shift slightly and a loop changes conformation.  This motion changes the geometry of the active site slightly but is NOT thought to be related to the allosteric transition.  J Mol Biol 204: 973-994.  [89125622]
ii	Motion is predominantly hinge
•	Tomato Bushy Stunt Virus (TBSV) Coat Protein .  [2TBV] 1 interdomain linkage,1 hinge, ~22 degree rotation. Motion is evident in comparing different subunits in the asymmetric unit. Single data bank identifier applies for both forms. This spherical virus contains 180 subunits arranged with icosahedral symmetry on a T=3 lattice. Each subunit, in turn, contains two major domains, the shell (S) and projection (P) domains that are linked by a peptide in an extended conformation.  The symmetry of the virus requires each subunit to fit into one of 3 different packing environments. One of the principal mechanisms for accommodating the different environments is a relative movement of the two domains by ~22 degrees.  This movement involves a simple hinge in the peptide connecting the S and P  domains.  J Mol Biol 171: 61. 
•	Lactoferrin.  [1LFH, 1LFG] 2 interdomain linkages, 2 hinges (in a beta-sheet), 53 degree rotation. See-saw between two interfaces. Lactoferrin is an iron transport protein. Upon binding iron, the two domains in the N-terminal half of the molecule close, in a motion involving two hinges. Upon closure the domains rotate 54 degrees essentially as rigid bodies. The axis of  rotation passes through the two beta-strands linking the domains. These strands contain hinges in the sense that three large torsion angle changes are responsible for the bulk of the motion while smaller torsion angle changes in neighboring residues  are responsible for the remainder of the motion. The rotation axes of these three torsion angle changes are nearly parallel to the axis of the overall 54 degrees rotation, so the local motion in the hinges can be directly related to the overall  motion. A crucial feature of the hinge residues is that they have very few packing constraints on their main-chain atoms. The domains make different packing contacts with each other in the open and closed forms. These contacts form two interdomain  interfaces arranged on either side of the hinges. Pivoting about the hinges produces a see-saw motion between the two interfaces. That is, when the domains close down, residues in the interface on one side of the hinges become buried and close-packed  and residues on the other side become exposed. The situation is reversed when the domains open up. Nature 344: 784-787.  J Mol Biol 234: 357-372.  [94047086]
•	Maltodextrin Binding Protein (MBP).  [1OMF, 2MBP] 3 interdomain linkages, 3 hinges, 35 degree rotation. The domain motion in the maltodextrin-binding protein is a 35 degree rotation about an axis through the hinge region, and there are large, localized torsion angle changes in the three peptides linking the domains. The positions of two of the hinges are structurally equivalent to the two hinges in lactoferrin.  Biochemistry 31: 10657-10663.  [93041761]
•	Lysine/Arginine/Ornithine (LAO) binding protein.  [1LST] 2 interdomain linkages, 2 hinges, 52 degree rotation. In the LAO binding protein there is a 52 degree rotation of the two domains, which involves only a few large torsion angle changes in regions structurally equivalent to the lactoferrin hinges. J Biol Chem 268: 11348-11355.  [93266593]
•	T4 lysozyme mutants: Ile3->Pro & Met6->Ile.  [1L96, 1L97] 2 hinges, at either end of interdomain helix, produce rotations up to 32 degrees. Depending on the crystal form, these 2 mutant lysozyme structures are either very similar to that of the wild-type or differ from it by a range of rigid-body domain rotations up to 32 degrees. There are two main hinge points for the domain motion.  They occur at the ends of the long helix that spans the domains. The second hinge involves 8 small torsion angle changes (between 9 and 15 degrees) spread throughout the C-terminal part of the helix, bending it by 3.3 A. As the location of the mutation is next to the hinge, the domain motion appears to be a consequence of the loss of close-packing created by the mutation and is an example of hinged motion created by reducing the number of steric constraints.  J Mol Biol 227: 917-933.  Nature 348: 263-266.  [91043097]
•	Adenylate Kinase (ADK).  [1AK3, 1AKE, 1ANK, 3ADK] 2 interdomain linkages and 4 hinges (one involves kinking helix). 60 degree rotation from 1st pair of hinges, 30 degree from 2nd pair, 90 degree total.  In large variants of adenylate kinase the AMP and ATP substrates are buried by a domain rotating by 90 degrees. The mobile domain is linked to the rest of the protein by two helices packed together in an antiparallel fashion. During the closure,  deformations take place in four localized regions, called joints, near the N and C termini of these helices. Three of these joints have simple motions that can be well approximated by rotations of three torsion angles, but the joint that makes  contact with the ligand involves motion throughout an extended loop: i.e. two torsions on either side of a reverse turn change significantly. The main chain atoms of the joints have few packing constraints. The first pair of joints is responsible for  approximately 30 degrees of the total rotation and the second pair for the remaining approximately 60 degrees. These movements carries along the regions between the joints, the two helices and the rest of the mobile domain, to a first approximation,  as rigid bodies.  ADK also has a shear motion when the first substrate, AMP, binds: i.e. in moving from the conformation of 3ADK to 1AK3, 3 helices with acrossed geometry shift 1-2 Angstroms to rearrange the geometry of thenucleotide binding site slightly. J Mol Biol 213: 627-630.  J Mol Biol 229: 494-501.  [93156056] J Mol Biol 217: 541-549.  Proteins: Struc Func Genet 19: 183-198. 
•	Catabolite Gene Activator Protein (CAP).  [3GAP] 1 interdomain linkage and 1 hinge. Comparison of subunits in the dimer reveals that the small domain has rotated ~30 degree closer to the large domain in one subunit. Motion is evident in comparing different subunits in the asymmetric unit. Single data bank identifier applies for both forms. J Mol Biol 198: 311-326. 
•	cAMP-dependent Protein Kinase (catalytic domain).  [1ATP, 1APM] 1st set of hinges, involving 3 interdomain linkages, produces 12 degree rotation of domain cores (with ~3 Angstrom shift). 2nd set of hinges produces further 6 degree rotation of a loop. 1 shearing interface between domains.  Structures of 2 conformations have been solved but only 1 has been deposited in the Protein Data Bank. The catalytic subunit of cAMP-dependent protein kinase has an elaborate multi-part hinged motion, which involves at least five distinct hinges, split into the two sets. Containing two domains, one large and one small, the structure of the catalytic subunit has been solved in binary and ternary complexes with an inhibitory peptide and in an apo form. In comparing the apo and either complex form, the core of the small domain rotates ~12 degrees relative to that of the large one. The small domain is  principally connected to the large domain through three roughly parallel peptide linkages, which deform as hinges upon closure. In addition, through the deformation of two more hinges a loop in the small domain near the binding pocket rotates a further 6  degrees down into the interdomain cleft. Partly because of the size of the interdomain cleft, which has to accommodate a 15 residue peptide, the protein kinase motion does not involve an extensive interdomain interface. There is, however, one helix in the small domain which moves in a shear fashion to maintain its contacts with the large domain throughout the motion.  Acta Cryst D 49: 381-388. 
•	Calmodulin.  [1CLL, 4CLN, 2BBM, 1CTR] 1 interdomain linkage, 1 hinge, ~150 degree rotation. Hinge involves long helix splitting into 2 helices (inclined at ~100 degrees) with strand in between. The unligated form of calmodulin contains two globular domains, connected by a long helix. NMR and X-ray structures of ligated calmodulin show the molecule binding to peptide helices with different sequences and the two domains closing around the peptide  far enough to make contact with each other. In this motion, the long interdomain helix, which is known to have only marginal stability in solution, partly unfolds to break into two helical segments connected by a 4-residue hinge region in an extended conformation. The angle between the axes of the two helical segments is ~100 degrees. As there is an additional twist around the helix axes, the total rotation of one domain relative to the other is upwards of 150 degrees. Calmodulin can bind  peptides with different sequences because of flexibility in the side chains that make contact with the peptide and by slightly shifting the relative placement of the domains through changes in the extent of the hinge region, which has consequently been  dubbed a variable 'expansion joint.' Science 262: 1718-1721.  [94082290] Science 257: 1251-1255.  [92390716] Science 256: 632-644.  
•	Glutamate Dehydrogenase (GDH). 13 degree rotation of 1 domain relative to other  J Mol Biol 234: 1131-1139. 
•	Diphtheria Toxin (DT).  [1DDT, 1MDT] 1 interdomain linkage, 1 hinge, 180 degree rotation, motions up to 65 Angstroms. Comparison of monomer and dimer reveal one domain has moved to a more open conformation in the latter.  Proc Natl Acad Sci U S A 91: 3127-3131.  [94211815]
•	Cell Adhesion Molecule CD2.  [1HNF, 1HNG] 1 interdomain linkage, 1 hinge, 20 degree rotation. Comparison of rat and human forms reveals rotation between two Ig-like domain. Structure 2: 755-766.  [95086863] Nature 360: 232-239.  [93063364]
•	Formate Dehydrogenase (FDH).  [2NAC, 2NAD] 2 interdomain linkages, 2 hinges, 7.5 degree rotation. Upon binding coenzyme, one domain rotates relative to the other to close over the active site. Each of the two hinges occurs in the middle of an alpha helix. J Mol Biol 236: 759-785.  [94157912]
•	Canine Lymphoma Immunoglobulin (Fc-Fab hinge). This crystal structure of an intact IgG molecule contains two Fab fragments and one Fc. The heavy-chain connection between each Fab and the Fc consists of a long, flexible, 'tether' polypeptide. In this crystal structure the two tether polypeptides  have different conformations. The hinge angle between Fc and Fab1 is ~65 degrees and that between Fc and Fab2 is ~115 degrees. The two Fab fragments also have difference dispositions of their constant and variable parts -- elbow angle differences.  Nature 360: 369-72.  [93078856]
•	Annexin V (breathing motion).  [1AVR, 1AVH] Annexin V has four domains (1, 2, 3, & 4). Domains 1 and 2 can move relative to 3 and 4. The motion involves the rotation of a few degrees and occurs in varying amounts throughout all known annexin structures. The function is unknown.  J Mol Biol 223: 683-704.  [92177413]
•	DNA Polymerase Beta (Pol Beta).  [1BPD, 2BPF, 2BPG] Pol Beta contains 4 domains: 8-kD, F, P, and T. In both apo and ternary complexes the F, P, and T domains are arranged in such a way as to form a cleft for the DNA. In apo form the 8-kD domain, which is connected to the F domain,  is moved away from the cleft. In the ternary complexes the 8-kD domain closes over the cleft to varying degrees through the motion of a singe flexible hinge of about 10 residues.  Science 264: 1930-5.  [94278498]
iii	Motion can not be fully classified at present 
•	TATA-box Binding Protein (TBP).  [1TBP] Twisting of a central sheet moves 2 domains ~10 degrees. Motion is evident in comparing different subunits in the asymmetric unit. Single data bank identifier applies for both forms. Nature 365: 520-527.  Proc Natl Acad Sci 90: 8174-8178.  [93376766] Nature 365: 512-520. 
•	Themolysin, Elastase, neutral proteases.  [1EZM, 4TMN] Bending interdomain helix  Biochemistry 31: 11310-11316.  J Biol Chem 266: 2864-2871. 
•	Elongation Factor Tu (EF-Tu).  [1ETU, 1EFT] Internal loop movements similar to those in ras protein (below) lead to large domain rearragements (90 degree rotation, 40 Ångstrom shifts) Structures of 2 conformations have been solved. Nature 365: 126-132.  Structure 1: 35-50.  [94248863]
iv	Motion is not hinge or shear 
•	Immunoglobulin (Fab Elbow Joint).  [1MCP, 4FAB, 2FBJ, 2FB4] Hinge motion in linking peptides. Ball & socket joint forms interface between domains. Range of rotations up to 50 degrees allowed. Data bank indentifiers for only 4 of the many representative immunoglobulin stuctures are indicated. The domain motion observed in the immunoglobulins involves, so far as is known at present, a unique combination of hinge and shear motions. In the immunoglobulins the VL domain is linked by an extended peptide to the CL domain, and VH  is similarly linked to CH1. VL and VH pack together, as do CL and CH1. The VL-VH dimer can freely rotate, relative to the CL-CH1 dimer, over a range of ~50 degrees in a manner described as 'elbow motion.' Elbow motion involves localized deformations in the two peptides that  link the V and C dimers. These deformations are similar to those in the hinged domain closures described in the previous sections. However, the elbow motion also involves an unusual type of shear motion: two large residues in CH1,  a Pro and Phe, pack  closely together, forming a 'ball,' and three residues in VH  spread out as part of a beta-sheet, forming a 'socket'. The three VH and two CH1 residues are packed together and move relative to each other in a manner similar to a socket moving over a ball. Unlike shear motions, which are characterized by close-packed interfaces of interdigitating sidechains, the ball-and-socket joint has a 'smooth' interface, in which the side chains do not interdigitate. This interface facilitates motion over a wide range  of relative orientations. It also permits greater flexibility than found in shear motions: the 'socket' residues can move up to 4.5 A relative to those in the 'ball,' rather than the 1.5 to 2.0 A displacement usually found at a shearing interface. Crit Rev Biochem 15: 291-384.  Nature 335: 188-190. 
v	Motion involves partial refolding of tertiary structure
•	Haemagglutinin.  [1hgf, 1htm] When this molecule is placed in low pH environment it undergoes a dramatic conformational change that almost amounts to the protein unfolding and then refolding with a new conformation. Parts of the protein move up to100 A.  Most of the protein is affected by the motion and there is no clear 'motionless' core. The most invariant part of the protein appears to be a helical segment (helix C) packed againt two equivalent helices in other subunits in a  a coiled-coil fashion. In the conformational change, residues N-terminal to this helix relocate and change into a helical conformation (to form helices A and B). This essentially extends helix C in the N-terminal direction.  Conversely, the helix directly connected to the C-terminal side of helix C  in the high-pH form (helix D) becomes partially an extended structure and relocates so that in the low pH-form it is antiparallel to helix C. Nature 371: 37-43.  [94352388]
•	HIV-1 Reverse Transcriptase.  [1HMI, 1HVT] Comparison of subunits shows very large rearrangement of 2 of the 4 domains which is accomodated by changes in loops and by unfolding of small 3 stranded beta-sheet.  Science 256: 1783-1790.  Proc Natl Acad Sci USA 90: 6320-6324. 
•	Serpins.  [5API, 1OVA] Translation at a helix-sheet interface results in the transformation of the tertiary structure by insertion of strand into sheet.  J Mol Biol 177: 531-556.  Prot Eng 3: 469-477.  J Mol Biol 221: 615-621.  Nature 355: 270-273. 
2	Proteins for which only one conformation is known but motion is suspected
i	Motion is predominantly shear
•	Phosphoglycerate Kinase (PGK).  [3PGK] Similar to hexokinase (XBAabx layering)  Proteins: Struc Func Genet 12: 133-144. 
•	Heat Shock Protein (HSP).  [1HSC] Similar to hexokinase (XBAabx layering)  Nature 346: 623. 
•	Actin.  [1ATN] Similar to hexokinase (XBAabx layering).  The second reference describes the structural similarity of actin and the heat-shock protein.  Nature 347: 37-44.  Proc Natl Acad Sci USA 88: 5041-5045. 
•	Aspartic Proteases, besides endothiapepsin: Penicllopepsin, Rhizopuspepsin, Chymosin, Porcine Pepsin.  [2APP,  2APR, 2PEP, 3CMS, 1PSG] Similar to endothiapepsin. Many intermediate conformations observed.  Proteins: Struc Func Genet 12: 158-170.  [92294166]
ii	Motion is predominantly hinge
•	Sulfate & Phosphate Binding Proteins.  [1SBP, 1ABH] Similar to MBP & lactoferrin. These are group-II periplasmic binding proteins.  J Mol Biol 200: 163-180.  Nature 347: 402-406.
•	Arabinose, Leucine, & Galactose Binding Proteins.  [2LBP, 2GBP, 1ABP] Similar to MBP & lactoferrin. However, these are group-I periplasmic binding proteins and are not as similar as group-II ones (above) are.  J Mol Biol 146: 341.  Science 242: 1290.  J Biol Chem 266: 5226-5237.  J Mol Biol 206: 171-191.  J Mol Biol 206: 193-207. 
•	Transferrins (N-terminal lobe).  [1TFD] Similar to lactoferrin  Acta Cryst B46: 763-771. 
•	Guanylate Kinase (GDK).  [1GKY] Similar to Adenylate Kinase.  J Mol Biol 211: 249. 
•	Porphobilinogen Deaminase.  [1PDA] Domains 1 and 2 similar to lactoferrin  Nature 359: 33-39. 
•	MAP Kinase ERK2. Similar to cAMP-dependent protein kinase  Nature 367: 704-710.  [94150699]
•	Thioredoxin reductase/Glutathione reductase.  [1TDE] Comparison of two indicates large conformational change involving 66 degree rotation of one domain  J Mol Biol 236: 800-816.  [94157914]
•	Oligopeptide-binding protein.  [1OLA, 1OLB] Two structures have been solved in closed conformation with peptide bound in deep interdomain cleft. Science 264: 1578-1581.  [94261830]
•	Glycerate Dehydrogenase (GDH).  [1GDH] Similiar to Formate Dehydrogenase (FDH)  J Mol Biol 236: 1123-40.  [94166078]
iii	Motion can not be fully classified at present 
•	Myosin. Closure of a nucleotide-binding cleft, with similarities to that of ADK, hypothesized to produce movements > 50 Angstrom  Science 261: 50-58. 
•	Transducin-a. Similar movements to EF-Tu and ras expected  Nature 366: 654-663. 
•	Topoisomerase I.   Nature 367: 138-146.  [94159070]
•	Ribose Binding Protein.  [2DRI] J Mol Biol 225: 155-175.  [92260530]
B	Motions of Fragments Smaller than Domains
1	Proteins for which open and closed conformations are known 
i	Motion is predominantly shear
•	Insulin.  [4INS] Helices shear by ~1.5 Angstrom. Structures of 2 conformations have been solved but only 1 has been deposited in the Protein Data Bank. Nature 302: 500-505. 
•	Thymidylate Synthase.  [3TMS, 2TSC] Small shear motion of helices packed onto central sheet.  Proteins: Struc Func Genet 8: 315.  Biochemistry 29: 6964-6977. 
•	Dihydrofolate Reductase (DHFR).  [4DFR, 5DFR] Small (~3 Angstrom) movement, shearing interface with hinges.  Biochemistry 30: 2227-2239. 
ii	Motion is predominantly hinge
•	Annexin V (Trp motion).  [1AVR, 2RAN, 1ANX] Large movements of 2 loops and end of a helix moves a buried trp residue 18 Angstrom to surface. Function of motion is unclear but it appears to be related to calcium concentration. The same change is seen in comparing annexin I (1AIN) to annexin V. Science 261: 1321-1324.  [93369587] J Mol Biol 234: 816-825.  [94076351]
•	Lactate Dehydrogenase (LDH).  [6LDH, 1LDM] Loop closure with 2 hinges, one in helix, moves CA atoms ~11 Angstrom. Upon binding lactate and NAD, lactate dehydrogenase undergoes a large conformational change that results in a surface loop moving roughly 10 A to cover the active site. In addition, there are appreciable movements (approximately 2 A) of five helices  and three other loops. The loop moves on two hinges separated by a relatively rigid type II turn. The first hinge has few steric constraints on it, and its motion can be well accounted for by large changes in two torsion angles, i.e. as in a classic  hinge motion. In contrast, the second hinge, which is part of a helix connected to the end of the loop, has many more constraints on it and distributes its deformation over more torsion angles. This novel motion involves the helix stretching and  splitting into alpha-helical and 3(10)-helical components and substantial side-chain repacking in the sense of 'cogs hopping between grooves' at its interface with the end of a neighboring helix. The loop is stabilized by five transverse (across  loop) hydrogen bonds. These are preserved, through the conformational change and through 17 lactate dehydrogenase sequences, more than the longitudinal hydrogen bonds down the sides of the loop. Through a network of contacts, many of them conserved  hydrophobic residues, the motion of the loop is propagated outward to structures that have no direct contact with the ligands. These moving structures are on the surface of the protein, and the whole protein can be subdivided into concentric shells  of increasing mobility.  J Mol Biol 102: 759-79.  J Mol Biol 220: 133-149.  [91295198]
•	Triose Phosphate Isomerase (TIM).  [2YPI, 3TIM, 6TIM] Loop closure with 2 hinges moves CA atoms ~ 7 Angstroms. Triose Phosphate Isomerase is one of the most extensively studied examples of loop closure. Three different variants of the enzyme have been analyzed crystallographically (chicken, yeast, and trypanosome)  and the enzyme has been solved in both open and closed conformations. The loop closure has also been studied by techniques ranging from site-directed mutagenesis to molecular dynamics.  TIM is a beta-barrel enzyme that contains 8 helices packed onto a  barrel of 8 sheets. An 11-residue loop running from an inner strand to an outer helix is flexible. When the enzyme binds its substrate the loop closes over the active site, shielding the substrate from water. The loop appears to close as a rigid lid,  stabilized by internal hydrogen bonds. Its motion involves movements of alpha carbons of up to 8 A. The closure involves the filling of a cavity near the base of the helix to which the loop is connected and the  formation of new hydrogen bonds and contacts. J Mol Biol 224: 1115-1126.  [91288486] Science 249: 1425-1428.  [90385280] Proteins 10: 93.  Biochemistry 29: 6619-25. 
•	Enolase.  [3ENL, 7ENL] Loop movements of ~7 Angstrom  Biochemistry 30: 2817. 
•	HIV-1 protease.  [4HVP, 3HVP, 5HVP] Two large loop regions, that together comprise one quarter of the structure, move CA atoms ~ 7 Angstrom  Science 246: 1149-52.  J Biol Chem 265: 14209-14219. 
•	Foot and mouth disease virus.  [1BBT] Comparing variants of virus shows movement of a surface loop Structures of 2 conformations have been solved but only 1 has been deposited in the Protein Data Bank. Nature 347: 569-72. 
•	Triglyceride Lipase.  [1TGL, 4TGL] 2 hinges on either side of a helix move CA atoms up to12 Angstrom. In one hinge a residue changes from an extended to a helical conformation.  Biochemistry  31: 1532-1541. 
•	Isocitrate Dehydrogenase (IDH).  [3ICD] Loop movements of ~2 Angstrom. Structures of 2 conformations have been solved but only 1 has been deposited in the Protein Data Bank. Biochemistry 32: 9317-9322. 
•	Malate Dehydrogenase (MDH).  [4MDH] Comparison of subunits shows a loop closure similar to LDH, moving atom CA atoms up to 8 Angstrom. Motion is evident in comparing different subunits in the asymmetric unit. Single data bank identifier applies for both forms. Biochemistry 28: 6065. 
•	ras Protein.  [4Q21, 6Q21] 2 loop movements move CA atoms up to 10 Angstrom (one movement includes helix attached to loop).  Science 247: 939-945.  Nature 345: 309. 
•	Seryl-tRNA synthetase.  [1SER, 1SES, 1SET] Two connected helices project out from protein like stalk. Upon binding tRNA these helices bend and rotate 20 degrees with respect to rest of protein.  Science 263: 1404-1410.  [94174274] Science 263: 1432-1436.  [94174279]
•	Hhal Methyltransferase.  [1HMY] Upon binding DNA, loop closure with 2 hinges moves atoms up to 25 Angstroms so that they can bind to DNA. Small shearing motions of other domain. Cell 74: 299-307.  [93945018] Cell 76: 357-369. 
•	Immunoglobulin 17/9 (CDR motion).  [1HIL, 1HIM] Upon binding antigen the H3 loop in this antibody switches in a different conformation. This moves alpha carbons by up to 4.6 A and sidechains atoms by up to 9 A. Science 255: 959-965.  [92188158] [94087724]
•	Cystatin.  [2CEW] Comparison of X-ray and NMR structure determinations shows that an 18 residue segment has changed from alpha-helical (X-ray) to beta-strand conformation (NMR). J Mol Biol 234: 1060-1069.  [94087720]
iii	Motion can not be fully classified at present 
•	CheY Protein.  [3CHY, 1CHN] J Biol Chem 266: 15511-15519.  [91332083] J Mol Biol 238: 489-495.  [94231569]
•	Virus MS2 coat protein .  [2MS2] Comparison of the protein in a assembled virus with a mutant version of the protein that is not involved in a assembly shows the movement of loop (85 to 87) that binds to RNA.  J Mol Biol 234: 620-639.  [94076340] Structure 3: 255-263. 
•	Glutamine Synthetase.  [2GLS, 2LGS, 1LGS] Small movements  Biochemistry 33: 675-681.  [94122178] J Biol Chem 264: 17681-17690.  [90036828]
2	Proteins for which only one conformation is known but motion is suspected
i	Motion is predominantly shear
ii	Motion is predominantly hinge
iii	Motion can not be fully classified at present 
•	Bacteriorhodopsin (bR).  [1BRD] This is a seven-helix transmembrane protein. When it is exposed to light, it goes through a photocycle.  In one intermediate in this cycle (M), movement is suspected in two helices (F and G). J Mol Biol 213: 899-929.  [90294303] EMBO J 12: 1-8.  [93154310]
C	Larger Movements than Domain Movements involving the Motion of Subunits
1	Proteins for which open and closed conformations are known 
i	Motion involves an allosteric transition
•	Hemoglobin (Hb).  [4HHB, 2HCO, 1HHO] Hemoglobin is a tetramer containing 2 copies of 2 (slightly) different subunits (alpha & beta). When oxygen binds to the deoxy form (the T-state), the heme ring slightly flattens.  This causes one helix (EF turn, F helix, FG turn) to move, and this, in turn, destabilizes salt bridges between this helix and a helix on another subunit. A new inter-subunit salt bridge configuration is formed (with in total fewer bridges). This switch of configurations at the subunit interface causes one pair of subunits (e.g. alpha-1 and beta-1) to rotate 15 degrees and translate 0.8 A relative to the other pair (producing the high-affinity R-state).  This in, in turn, affects the interactions about the heme in other subunits, giving rise to cooperative oxygen binding.  Sci Am 239: 92-125.  Quart Rev Biophys 22: 139-237.   J Mol Biol 129: 175-220.  J Mol Biol 175: 159-174. 
•	Aspartate Transcarbamoylase (ATCase).  [8ATC, 5AT1] Quaternary structure motion: ATCase is composed of 6 regulatory subunits and 6 catalytic subunits. The 6 catalytic subunits are arranged as a sandwich (i.e. dimer) of 2 trimers, sharing the same (3-fold) symmetry axis. The 6 regulatory subunits are divided into three dimers, each of which runs between both sides of the 'catalytic trimer sandwich.' In moving from the low to high affinity state (T to R), the regulatory dimers rotate by ~15 degrees about their dimer axes. Both parts of the catalytic  trimer sandwich, in turn, separate by ~12 A along the 3-fold axis and rotate by ~10 degrees about this same axis. Tertiary structure motion: Each catalytic subunit is composed of two domains (aspartate and carbamoyl phosphate), and these domains close  around the active site in the T to R transition, thus coupling tertiary structure changes to quaternary structure changes. The domain closure involves (local) motions of up to 2 A. There is one interdomain linkage and to a large degree the domain closure  can be considered to operate by a hinge mechanism. There are, however, additional loop movements in both domains (the 80s and 240s loops).  Biochemistry 29: 7691-7701.  [91104727] Proc Natl Acad Sci 89: 5281-5285.  [92302228] 
•	Glycogen Phosphorylase (GP).  [9GPB, 1GPB] Quaternary Structure Changes: In the low to high affinity transition (T to R), the two subunits in a GP dimer rotate relative to each other by ~10 degrees. There are two main contact points between the subunits: the tower helices and the Cap/alpha2 contact. The subunit rotation is perpendicular to the dimer twofold and occurs about the Cap/alpha2 contact. It moves together atoms in this region by ~1 A and moves them apart  near the tower helices by ~3 A. The tower helix interface completely repacks, changing the helix packing angles by ~20 degrees. Tertiary Structure Changes: the change in orientation of the tower helices causes a loop near the active site (the 280s loop)  to disorder in the R form. This prevents blockage of the active site.  Nature 340: 609-616.  [89365154] J Biol Chem 265: 2409-2412.  [90153846]
•	Phosphofructokinase.  [1PFK, 5PFK] PFK is a tetramer of four identical subunits, arranged into two dimers. There is a large interface (~2200 sq. A) between subunits in each dimer, and a smaller interface (~1500 sq. A) between dimers.  Quaternary Structure Changes: In the transition between high and low affinity forms, (R to T), the dimers rotate 7 degrees relative to each other. This causes changes in the smaller interface. A layer of water molecules bridging two beta-strands is expelled, leading to the creation of more hydrogen bonds between the dimers.  Tertiary Structure Changes: A loop near the substrate binding site and the small dimer interface (the 6-F loop) changes shape considerably. There are also some small shearing motions of helices in each subunit (8 and 9).  J Mol Biol 191: 713-720.  [87112731] Nature 343: 140-145.  [90114433] Curr Opin Struc Biol 1: 773-779. 
ii	Motion does not involves an allosteric transition
•	Immunoglobulin 50.1 (VL-VH).  [1GGC, 1GGI] Upon binding peptide, VH rotates 15 degrees and translates 2.7 A relative to VL  Proc Natl Acad Sci U S A 90: 6325-6329.  [93317674] Structure 1: 83-93. 
•	Immunoglobulin BV04-01 (VL-VH).  [1NBV, 1CBV] Upon binding DNA, VH rotates 7.5 degrees and translates 0.75 A relative to VL. There are also loop motions in the CDRs.  Proteins 11: 159-175.  [92086633]
2	Proteins for which only one conformation is known but motion is suspected
i	Motion involves an allosteric transition
ii	Motion does not involves an allosteric transition
•	F1-ATPase. Six globular subunits (3 alpha and 3 beta) are arranged around a long central helix (gamma subunit). Because of the asymmetries in the orientation of the alpha and beta subunits, they are hypothesized to rotate around the central helix.  Also comparison of the beta subunits shows that in one of them (beta-E) a sheet has partially unfolded.  Nature 370: 621-628.  [94344236]
•	GroEL. Probable subunit and domain motions. Nature 371: 578-586.  [95021709]
•	Polymerase Processivity Factor PCNA.  [1PLQ] PCNA subunits are arranged in a ring-like trimer, which is believed to clamp around DNA. For such a clamp to attach and unattach to DNA motion of the subunits is necessary.  Cell 79: 1233-43.  [95094298]