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C Chothia

Publications and source records attributed to C Chothia.

At least 19 recordsLinked to original sources
PubMed1992

Structural repertoire of the human VH segments.

The VH gene segments produce the part of the VH domains of antibodies that contains the first two hypervariable regions. The sequences of 83 human VH segments with open reading frames, from several individuals, are currently known. It has been shown that these sequences are likely to form a high proportion of the total human repertoire and that an individual's gene repertoire produces about 50 VH segments with different protein sequences. In this paper we present a structural analysis of the amino acid sequences produced by the 83 segments. Particular residue patterns in the sequences of V domains imply particular main-chain conformations, canonical structures, for the hypervariable regions. We show that, in almost all cases, the residue patterns in the VH segments imply that the first hypervariable regions have one of three different canonical structures and that the second hypervariable regions have one of five different canonical structures. The different observed combinations of the canonical structures in the first and second regions means that almost all sequences have one of seven main-chain folds. We describe, in outline, structures of the antigen binding site loops produced by nearly all the VH segments. The exact specificity of the loops is produced by (1) sequence differences in their surface residues, particularly at sites near the centre of the combining site, and (2) sequence differences in the hypervariable and framework regions that modulate the relative positions of the loops.

Amino Acid Sequence↗
PubMed1992

Domain closure in mitochondrial aspartate aminotransferase.

The subunits of the dimeric enzyme aspartate aminotransferase have two domains: one large and one small. The active site lies in a cavity that is close to both the subunit interface and the interface between the two domains. On binding the substrate the domains close together. This closure completely buries the substrate in the active site and moves two arginine side-chains so they form salt bridges with carboxylate groups of the substrate. The salt bridges hold the substrate close to the pyridoxal 5'-phosphate cofactor and in the right position and orientation for the catalysis of the transamination reaction. We describe here the structural changes that produce the domain movements and the closure of the active site. Structural changes occur at the interface between the domains and within the small domain itself. On closure, the core of the small domain rotates by 13 degrees relative to the large domain. Two other regions of the small domain, which form part of the active site, move somewhat differently. A loop, residues 39 to 49, above the active site moves about 1 A less than the core of the small domain. A helix within the small domain forms the "door" of the active site. It moves with the core of the small domain and, in addition, shifts by 1.2 A, rotates by 10 degrees, and switches its first turn from the alpha to the 3(10) conformation. This results in the helix closing the active site. The domain movements are produced by a co-ordinated series of small changes. Within one subunit the polypeptide chain passes twice between the large and small domains. One link involves a peptide in an extended conformation. The second link is in the middle of a long helix that spans both domains. At the interface this helix is kinked and, on closure, the angle of the kink changes to accommodate the movement of the small domain. The interface between the domains is formed by 15 residues in the large domain packing against 12 residues in the small domain and the manner in which these residues pack is essentially the same in the open and closed structures. Domain movements involve changes in the main-chain and side-chain torsion angles in the residues on both sides of the interface. Most of these changes are small; only a few side-chains switch to new conformations.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1992

beta-Trefoil fold. Patterns of structure and sequence in the Kunitz inhibitors interleukins-1 beta and 1 alpha and fibroblast growth factors.

Previous crystallographic analyses of the Kunitz inhibitors from soybean. Erythrina caffra and wheat, the interleukins-1 beta and 1 alpha and the acidic and basic fibroblast growth factors have shown that they contain a most unusual fold. It is formed by six two-stranded hairpins. Three of these form a barrel structure and the other three are in a triangular array that caps the barrel. The arrangement of the secondary structures gives the molecules a pseudo 3-fold axis. Although the different proteins have very similar structures, many of their sequences have no significant similarities overall. The structural determinants of this fold are described and discussed in this paper. The barrels in the different proteins have the same geometrical features: six strands tilted at 56 degrees to the barrel axis; a barrel diameter of 16 A, and the beta-sheet hydrogen bonded so that it is staggered with a shear number of 12. These features fit McLachlan's equations for ideal barrels formed by beta-sheets. The wide diameter of the barrels is filled by layers of residues that, while not identical in the different proteins, are, in almost all cases, large. The structure of the triangular array of hairpins is determined by the coiling of the strands and the packing of hairpin residues against each other and against residues from the interior of the barrel. The major sequence requirements of this fold are large or medium hydrophobic residues at 18 buried sites. In the different structures the total volume of these residues is 3000 (+/- 120) A. The polyhedron model of protein architecture is used to demonstrate that the main, and in particular the symmetrical, features of this fold arise from the ideal and equal packing of six hairpins, modified only slightly to form hydrogen bonds between the hairpins.

Amino Acid Sequence↗
PubMed1991

Serpin tertiary structure transformation.

Previous crystallographic analyses have demonstrated that proteolytic cleavage of the serpins can result in a dramatic transformation of their tertiary structure. Some 16 residues on the amino terminal side of the cleavage site are inserted into a large beta-sheet to become a central strand, separating the two cleaved residues by about 70 A. We have determined, in outline, the nature of the conformational change responsible for this transformation. After cleavage, a fragment of the protein, consisting of an alpha-helix and three strands of beta-sheet, moves away from the rest of the structure to make the space for the new strand. This movement involves a new type of structural change: sheet residues in the small fragment slide along grooves in an alpha-helix that belongs to the rest of the protein. The general conservation of residues in the regions between the small fragment and the rest of the protein imply that the same mechanism will be found in all serpins that undergo this tertiary structure transformation.

Amino Acid Sequence↗
PubMed1991

Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase.

As shown in previous crystallographic investigations, 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. We demonstrate by a new fitting procedure that 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.

Amino Acid Sequence↗
PubMed1991

The structural homology of amicyanin from Thiobacillus versutus to plant plastocyanins.

The complete amino acid sequence of the blue copper protein amicyanin of Thiobacillus versutus, induced when the bacterium is grown on methylamine, has been determined as follows: QDKITVTSEKPVAAADVPADAVVVGIEKMKYLTPEVTIKAGETVYWVNGEVMPHNVA FKKGIVGEDAFRGEMMTKDQAYAITFNEAGSYDYFCTPHPFMRGKVIVE. The four copper ligand residues in this 106-residue-containing polypeptide chain are His54, Cys93, His96, and Met99. The Thiobacillus amicyanin is 52% similar to the amicyanin of Pseudomonas AM1, the only other copper protein known with the same spacing between the second histidine ligand and the methionine ligand. T. versutus amicyanin contains no cysteine bridge and is more closely related to the plant copper protein plastocyanin than to the bacterial copper protein azurin. Alignment of the two known amicyanin sequences with the consensus sequence of the plastocyanins and comparison with the known three-dimensional structure of poplar leaves plastocyanin reveals that the bacterial proteins have the same overall structure with two beta-sheets packed face to face. The major structural differences between the amicyanins and the plastocyanins appear to be located in two of the five loops that connect the six identified beta-strands of the amicyanins. The first of these two loops, connecting strands F and G, contains a ligand histidine and must have a different conformation from the same loop in the plastocyanins because it is shorter by two amino acids. Further differences occur in the loop connecting the strands D and E. This loop contains only 17 residues in amicyanin whereas the corresponding loop of plastocyanin contains 25 residues. Despite these differences the amicyanins appear much closer related to the plastocyanins than to the azurins. The present findings demonstrate that the occurrence of blue copper proteins with clearly plastocyanin-like features is not restricted to photosynthetic redox chains.

Amino Acid Sequence↗
PubMed1991

Asymmetry in protein structures.

The asymmetry of L-amino acids determines the asymmetrical features of alpha-helices and beta-sheets. These in turn determine two principal aspects of the three-dimensional structure of proteins: the preferred ways in which alpha-helices and beta-sheets pack together, and certain topological features of the paths followed by polypeptide chains through structures. Though the asymmetrical nature of amino acids plays the central role in determining the asymmetrical aspects of protein structures, it has little or no influence on the next level of biological structures--assemblies of protein molecules.

Amino Acids↗
PubMed1990

Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the VH domains of immunoglobulins.

Analysis of the immunoglobulins of known structure reveals systematic differences in the position and main-chain conformation of the second hypervariable region of the VH domain (H2). We show that the major determinant of the position of H2 is the size of the residue at site 71, a site that is in the conserved framework of the VH domain. It is likely that for about two thirds of the known VH sequences the size of the residue at this site is also a major determinant of the conformation of H2. This effect can override the predisposition of the sequence, as in the case of the H2 loop of J539, which is an exception to the rules relating sequence and conformation of short hairpin loops. Understanding the relationship between the residue at position 71 and the position and conformation of H2 has applications to the prediction and engineering of antigen-binding sites of immunoglobulins.

Amino Acid Sequence↗
PubMed1989

Structural principles of alpha/beta barrel proteins: the packing of the interior of the sheet.

Alpha/beta barrel structures very similar to that first observed in triose phosphate isomerase are now known to occur in 14 enzymes. To understand the origin of this fold, we analyzed in three of these proteins the geometry of the eight-stranded beta-sheets and the packing of the residues at the center of the barrel. The packing in this region is seen in its simplest form in glycolate oxidase. It consists of 12 residues arranged in three layers. Each layer contains four side chains. The packing of RubisCO and TIM can be understood in terms of distortions of this simple pattern, caused by residues with small side chains at some of the positions inside the barrel. Two classes of packing are found. In one class, to which RubisCO and TIM belong, the central layer is formed by a residue from the first, third, fifth, and seventh strands; the upper and lower layers are formed by residues from the second, fourth, sixth, and eighth strands. In the second class, to which GAO belongs, this is reversed: it is side chains from the even-numbered strands that form the central layer, and side chains from the odd-numbered strands that form the outer layers. Our results suggest that not all proteins with this fold are related by evolution, but that they represent a common favorable solution to the structural problems involved in the creation of a closed beta barrel.

Alcohol Oxidoreductases↗
PubMed1989

Structural determinants of the conformations of medium-sized loops in proteins.

Loops are integral components of protein structures, providing links between elements of secondary structure, and in many cases contributing to catalytic and binding sites. The conformations of short loops are now understood to depend primarily on their amino acid sequences. In contrast, the structural determinants of longer loops involve hydrogen-bonding and packing interactions within the loop and with other parts of the protein. By searching solved protein structures for regions similar in main chain conformation to the antigen-binding loops in immunoglobulins, we identified medium-sized loops of similar structure in unrelated proteins, and compared the determinants of their conformations. For loops that form compact substructures the major determinant of the conformation is the formation of hydrogen bonds to inward-pointing main chain atoms. For loops that have more extended conformations, the major determinant of their structure is the packing of a particular residue or residues against the rest of the protein. The following picture emerges: Medium-sized loops of similar conformation are stabilized by similar interactions. The groups that interact with the loop have very similar spatial dispositions with respect to the loop. However, the residues that provide these interactions may arise from dissimilar parts of the protein: The conformation of the loop requires certain interactions that the protein may provide in a variety of ways.

Binding Sites↗
PubMed1988

The outline structure of the T-cell alpha beta receptor.

From an analysis of the immunoglobulins of known structure we derive a list of 40 sites crucial for the conserved structure of the variable domains. We show that, with marginal exceptions, the sequences of the T-cell alpha beta receptors contain, at sites homologous to these 40, the same or very similar residues. Thus the V alpha-V beta dimer has a framework structure very close to that of the immunoglobulins. Further comparisons show that parts of the surface of the V alpha-V beta framework are hypervariable. They also show that the loops that form the antigen-binding site are similar in size to those commonly found in the immunoglobulins but have different conformations. Only limited sequence variations occur in the first loop of the antigen-binding site in both V alpha and V beta. This, and their geometrical arrangement, suggest that they mainly interact with the MHC proteins.

Amino Acid Sequence↗
PubMed1988

Surface, subunit interfaces and interior of oligomeric proteins.

The solvent-accessible surface area (As) of 23 oligomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. As is correlated with the protein molecular weight, and a power law predicts its value to within 5% on average. The accessible surface of the average oligomer is similar to that of monomeric proteins in its hydropathy and amino acid composition. The distribution of the 20 amino acid types between the protein surface and its interior is also the same as in monomers. Interfaces, i.e. surfaces involved in subunit contacts, differ from the rest of the subunit surface. They are enriched in hydrophobic side-chains, yet they contain a number of charged groups, especially from Arg residues, which are the most abundant residues at interfaces except for Leu. Buried Arg residues are involved in H-bonds between subunits. We counted H-bonds at interfaces and found that several have none, others have one H-bond per 200 A2 of interface area on average (1 A = 0.1 nm). A majority of interface H-bonds involve charged donor or acceptor groups, which should make their contribution to the free energy of dissociation significant, even when they are few. The smaller interfaces cover about 700 A2 of the subunit surface. The larger ones cover 3000 to 10,000 A2, up to 40% of the subunit surface area in catalase. The lower value corresponds to an estimate of the accessible surface area loss required for stabilizing subunit association through the hydrophobic effect alone. Oligomers with small interfaces have globular subunits with accessible surface areas similar to those of monomeric proteins. We suggest that these oligomers assemble from preformed monomers with little change in conformation. In oligomers with large interfaces, isolated subunits should be unstable given their excessively large accessible surface, and assembly is expected to require major structural changes.

Amino Acids↗
PubMed1988

Elbow motion in the immunoglobulins involves a molecular ball-and-socket joint.

Studies by electron microscopy, fluorescence polarization, hydro-dynamics and X-ray crystallography have demonstrated the ability of different parts of immunoglobulin molecules to move relative to each other. This movement facilitates the multiple interactions that antibodies make with polyvalent antigens and effector proteins. Comparisons of the atomic structures of immunoglobulins of the same sequence in different crystal environments, and of those with different sequences, have shown that the movements involve local changes in the conformation of the peptides linking different domains. These changes occur in (1) the hinge regions that link the Fab fragment to the Fc, and (2) the switch regions that link the VL-VH dimer to the CL-CH1 dimer. We show here that in immunoglobulins of known structure, the movement of the VL-VH dimer relative to the CL-CH1 dimer also involves the interactions of three VH and two CH1 residues that form the molecular equivalent of a ball-and-socket joint. The almost absolute conservation in the sequences of immunoglobulins and T-cell receptors of the residues that form these interactions suggests that this is a general feature of functional importance.

Crystallography↗