Table 1: Proteins that Undergo Domain Movements

(A)	Proteins for which open and closed conformations are known a b
(i)	Domain motion is predominantly shear				
Citrate Synthase c	1CTS
3CTS	Remington et al., 1982;
Lesk & Chothia, 1984	Shear motions at many helix-helix interfaces shift mainchain atoms up to 10 Å	
Aspartate Amino 
Transferase (AAT) c	9AAT
1AMA	McPhalen et al., 1992	Shear motion at 2 interfaces combined with hinge in a kinked helix.	
Trp Repressor c	1WRP
2WRP
3WRP	Lawson et al.,1988	Shear motion between 2 helices adjusts position of helix-turn-helix reading head domain to enable it to bind DNA	
Hexokinase c	2YHX
1HKG	Bennett & Steitz, 1978, 1980;
Lesk & Chothia, 1984  	Shear motion with XBAaba layering. Prominent crossed helices at interdomain interface. 	
Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) c	1GD1
2GD1	Skarzynski & Wonacott, 1988	Shear motion with XBAaba layering.	
Alcohol Dehydrogenase (ADH) c	8ADH
6ADH	Eklund et al.,1981; 
Colonna-Cesari et al., 1986	Shear motion with XBAaba layering and 2 hinges.	
Endothiapepsin	4APE
5ER2	Sali et al., 1989; 1992
	Small shearing motion at 1 interface between domains (17° rotation and 1 Å displacement)	
(ii)	Domain motion is predominantly hinge				
Tomato Bushy Stunt Virus (TBSV) Coat Protein c e	2TBV	Olson et al., 1983	1 interdomain linkage,1 hinge, ~22° rotation.	
Lactoferrin c	1LFH
1LFG	Anderson et al., 1990;
Gerstein et al., 1993b	2 interdomain linkages, 2 hinges (in a b-sheet), 53° rotation. See-saw between two interfaces. 	
Maltodextrin Binding Protein
(MBP) c	1OMF
2MBP	Sharff et al., 1992;
	3 interdomain linkages, 3 hinges, 35° rotation.	
Lysine/Arginine/Ornithine (LAO) binding protein c	1LST	Oh et al., 1993	2 interdomain linkages, 2 hinges, 52° rotation.	
T4 lysozyme mutants: 
Ile3ÆPro & Met6ÆIle c	1L96
1L97	Dixon et al., 1992;
Faber & Matthews, 1991	2 hinges, at either end of interdomain helix, produce rotations up to 32°.	
Adenylate Kinase (ADK) c g	1AK3
1AKE	Schulz et al., 1990;
Gerstein et al., 1993a	2 interdomain linkages and 4 hinges (one involves kinking helix). 60° rotation from 1st pair of hinges, 30° from 2nd pair, 90° total.  	
Catabolite Gene Activator Protein (CAP) e	3GAP	Weber & Steitz, 1987	1 interdomain linkage and 1 hinge. Comparison of subunits in the dimer reveals that the small domain has rotated ~30° closer to the large domain in one subunit.	
cAMP-dependent Protein Kinase (catalytic  domain) c d	1ATP
1APM	Karlsson et al., 1993	1st set of hinges, involving 3 interdomain linkages, produces 12° rotation of domain cores  (with ~3 Å shift). 2nd set of hinges  produces further 6° rotation of  a loop. 1 shearing interface between domains.	
Calmodulin c	1CLL
4CLL
2BBM	Ikura et al., 1992; 
Meador et al., 1992, 1993	1 interdomain linkage, 1 hinge, ~150° rotation. Hinge involves long helix splitting into 2 helices (inclined at ~100°)  with strand in between.	
Glutamate Dehydrogenase		Stillman et al., 1993	13° rotation of 1 domain relative to other	
(iii)	Domain motion is not predominantly a hinge or shear mechanism				
Immunoglobulins c h	2FB4
1MCP	Bennett & Huber, 1984;
Lesk & Chothia,  1988;	Hinge motion in linking peptides. 
Ball & socket joint forms interface between domains.
Range of rotations up to 50° allowed.  	
Serpins	5API 1OVA	Loebermann et al., 1984  
Engh et al., 1990 
Stein & Chothia, 1991
Mottonen et al., 1992	Translation at a helix-sheet interface results in the transformation of the tertiary structure by insertion of strand into sheet. 	
(iv)	Domain motion can not be fully classified at present f				
HI V-1 Reverse Transcriptase	1HMI
1HVT	Kohlstaedt et al., 1992;
Jacobo-Molina et al., 1993	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 b-sheet. 	
TATA-box Binding Protein
(TBP) e	1TBP	Kim et al., 1993a, 1993b;
Chasman et al., 1993	Twisting of a central sheet moves 2 domains ~10°. 	
Themolysin, Elastase,  neutral proteases 	1EZM
4TMN	Holland et al., 1992;
Thayer et al., 1991	Bending interdomain helix	
Elongation Factor Tu (EF-Tu) d	1ETU	Berchtold et al., 1993;
Kjeldgaard et al., 1993	Internal loop movements similar to those in ras protein (below) lead to large domain rearragements (90° rotation, 40Å shifts) 	

(B)	Proteins for which only one conformation is known
(i)	Domain motion is predominantly shear				
Phosphoglycerate Kinase (PGK) c	3PGK	Harlos et al., 1992	Similar to hexokinase (XBAabx layering)	
Heat Shock Protein 	1HSC	Flaherty et al. ,1990 	Similar to hexokinase (XBAabx layering)	
Actin	1ATN	Kabsch et al. ,1990;
Flaherty et al., 1991  i	Similar to hexokinase (XBAabx layering)	
Aspartic Proteases, besides endothiapepsin: Penicllopepsin, Rhizopuspepsin, Chymosin, Porcine Pepsin	2APP
2APR
2PEP
3CMS
1PSG	Sali et al., 1992	Similar to endothiapepsin	
(ii)	Domain motion is predominantly hinge				
Sulfate & Phosphate Binding Proteins	1SBP
1ABH	Luecke & Quiocho, 1990; 
Pflugrath & Quiocho, 1988	Similar to MBP & lactoferrin. These are group-II periplasmic binding proteins.	
Arabinose, Leucine, & Galactose Binding Proteins	2LBP
2GBP
1ABP	Gilliland  & Quiocho, 1981; 
Vyas et al., 1988, 1991;
Sack et al., 1989a,b  	Similar to MBP & lactoferrin. However, these are group-I periplasmic binding proteins and are not as similar  as group-II ones (above) are.	
Transferrins (N-terminal lobe)	1TFD	Sarra et al., 1990	Similar to lactoferrin	
Guanylate Kinase (GDK)	1GKY	Stehle & Schulz, 1990	Similar to ADK	
Porphobilinogen Deaminase 	1PDA	Louie et al., 1992	Domains 1 and 2 similar to lactoferrin 	
(iii)	Domain motion can not be classified at present f	
Myosin		Rayment et al., 1993	Closure of a nucleotide-binding cleft, with similarities to that of ADK,  hypothesized to produce movements > 50 Å	
Transducin-a		Noel et al., 1993	Similar movements to EF-Tu and ras expected	
(C)	Proteins known in two conformations which involve movements of fragments smaller than domains a
(i)	Motion is predominantly shear	
Insulin d	4INS	Chothia et al., 1983	Helices shear by ~1.5 Å.	
Thymidylate Synthase	3TMS
2TSC	Perry et al., 1990;
Montfort et al., 1990	Small shear motion of helices packed onto central sheet.	
Dihydrofolate Reductase
(DHFR)	4DFR
5DFR	Bystroff et al., 1991	Small (~3 Å) movement, shearing interface with hinges.	
(ii)	Motion is predominantly hinge	
Annexin V	1AVR
1RAN	Sopkova et al., 1993;
Concha, et al., 1993	Large movements of 2 loops and end of a helix moves a buried trp residue 18Å to surface.	
Lactate Dehydrogenase (LDH)	6LDH
1LDM	White et al., 1976;
Gerstein & Chothia, 1991	Loop closure with 2 hinges, one in helix, moves Ca atoms ~11 Å	
Triose Phosphate Isomerase
(TIM)	2YPI
3TIM
6TIM	Lolis & Petsko, 1990;
Joseph et al., 1990;
Wirenga et al., 1991	Loop closure with 2 hinges moves Ca atoms ~ 7Å	
Enolase	3ENL
7ENL	Lebioda & Stec, 1991	Loop movements of ~7 Å	
HIV-1 protease 	4HVP
3HVP
5HVP	Miller et al., 1989;
Fitzgerald et al., 1990	Two large loop regions, that together comprise one quarter of the structure, move Ca atoms ~ 7Å	
Foot and mouth disease virus d	1BBT	Parry et al., 1990	Comparing variants of virus shows movement of a surface loop	
Triglyceride Lipase	1TGL
4TGL	Derewenda et al., 1992;	2 hinges on either side of a helix move Ca atoms up to12 Å. In one hinge a residue changes from an extended to a helical conformation. 	
Isocitrate Dehydrogenase d	3ICD	Stoddard & Koshland, 1993	Loop movements of ~2 Å	
Malate Dehydrogenase
(MDH) e	4MDH	Birktoft et al., 1989	Comparison of subunits shows a loop closure similar to LDH, moving atom Ca atoms up to 8 Å.	
ras Protein	4Q21
6Q21	Milburn et al., 1990;
Sclichting et al., 1990	2 loop movements move Ca atoms up to 10 Å
(one movement includes helix attached to loop).  	

a  When both open and closed forms are known, we refer to the papers that describe the structure comparisons. Further references to the individual open and closed structures can be found in these papers.  b  Allosteric proteins are not included because these proteins have motions that involve extensive repacking of interfaces (see Perutz, 1989 for a review). Such repacking involves high-energy conformational transitions distinctly different from the hinge and shear mechanisms.  c  Indicates proteins discussed in detail in the text.  d  Structures of 2 conformations have been solved but only 1 has been deposited in the Protein Data Bank.  e  Motion is evident in comparing different subunits in the asymmetric unit. Single data bank identifier applies for both forms.  f  It is not possible to classify some domain motions at present because full sets of coordinates or detailed analyses are not yet available.  g  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 a crossed geometry shift 1-2 Å to rearrange the geometry of the nucleotide binding site slightly (Diederichs & Schulz, 1991).  h  Data bank indentifiers for only two of the many representative immunoglobulin stuctures are indicated.  i  This paper describes the structural similarity of actin and the heat-shock protein.