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C Chothia

Publications and source records attributed to C Chothia.

At least 91 records · Page 5Linked to original sources
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↗
PubMed1987

Canonical structures for the hypervariable regions of immunoglobulins.

We have analysed the atomic structures of Fab and VL fragments of immunoglobulins to determine the relationship between their amino acid sequences and the three-dimensional structures of their antigen binding sites. We identify the relatively few residues that, through their packing, hydrogen bonding or the ability to assume unusual phi, psi or omega conformations, are primarily responsible for the main-chain conformations of the hypervariable regions. These residues are found to occur at sites within the hypervariable regions and in the conserved beta-sheet framework. Examination of the sequences of immunoglobulins of unknown structure shows that many have hypervariable regions that are similar in size to one of the known structures and contain identical residues at the sites responsible for the observed conformation. This implies that these hypervariable regions have conformations close to those in the known structures. For five of the hypervariable regions, the repertoire of conformations appears to be limited to a relatively small number of discrete structural classes. We call the commonly occurring main-chain conformations of the hypervariable regions "canonical structures". The accuracy of the analysis is being tested and refined by the prediction of immunoglobulin structures prior to their experimental determination.

Amino Acid Sequence↗
PubMed1987

Interior and surface of monomeric proteins.

The solvent-accessible surface area (As) of 46 monomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. The As of these proteins can be determined to within 1 to 2% and that of their individual residues to within 10 to 20%. The As values of proteins are correlated with their molecular weight (Mr) in the range 4000 to 35,000: the power law As = 6.3 M0.73 predicts protein As values to within 4% on average. The average water-accessible surface is found to be 57% non-polar, 24% polar and 19% charged, with 5% root-mean-square variations. The molecular surface buried inside the protein is 58% non-polar, 39% polar and 4% charged. The buried surface contains more uncharged polar groups (mostly peptides) than the surface that remains accessible, but many fewer charged groups. On average, 15% of residues in small proteins and 32% in larger ones may be classed as "buried residues", having less than 5% of their surface accessible to the solvent. The accessibilities of most other residues are evenly distributed in the range 5 to 50%. Although the fraction of buried residues increases with molecular weight, the amino acid compositions of the protein interior and surface show no systematic variation with molecular weight, except for small proteins that are often very rich in buried cysteines. From amino acid compositions of protein surfaces and interiors we calculate an effective coefficient of partition for each type of residue, and derive an implied set of transfer free energy values. This is compared with other sets of partition coefficients derived directly from experimental data. The extent to which groups of residues (charged, polar and non-polar) are buried within proteins correlates well with their hydrophobicity derived from amino acid transfer experiments. Within these three groups, the correlation is low.

Amino Acid Sequence↗
PubMed1987

Determinants of a protein fold. Unique features of the globin amino acid sequences.

The three-dimensional structures of globins are known, from crystallographic analyses, to be very similar. Their amino acid sequences, however, differ greatly. Only two residues are absolutely conserved in all sequences, and the residue identities of some pairs of sequences are only 16%. We have determined the nature and exact extent of the sequence variations and the extent to which the conserved features of the globin sequences are unique to this family. The 226 globin sequences now known were aligned and analysed. Because distantly related protein sequences cannot be aligned correctly without the use of structural data, we developed a method that incorporated structural information into the alignment procedure. Analysis of the aligned sequences show that: (1) Although individual chains vary in size between 132 and 157 residues, deletions and insertions result in there being only 102 residue sites common to all globins. These sites form six separate regions. Insertions and deletions between these regions means that their separations can vary in different sequences. (2) Within the conserved regions there are 32 sites that almost always contain hydrophobic residues. In the known structures, these sites are in the protein interior. We measured the variations in the size of the residues that occur in the 226 sequences at these sites. At six sites the residues differ in size by less than 40 A3, at 11 sites they differ by 40 to 100 A3, and at 15 sites they differ by more than 100 A3. There are two other conserved buried sites: one contains the His linked to the haem iron and the other usually contains a His involved with the haem ligand. (3) Within the conserved regions there are another 32 sites that are almost always occupied by charged, polar or small non-polar (Gly or Ala) residues. In the known structures, these sites are on the protein surface. To determine the extent to which the conserved features found for the globin sequences are unique to that protein family, the following procedure was used. The six conserved regions, and the residue restrictions that occur at the 66 sites within these regions, were encoded into two "templates". One was based only on the sequences so far determined; the other was extended to include as yet unobserved substitutions that seemed plausible on the basis of size, hydrophobicity and polarity. Each of the 3286 non-globin sequences in the data bank was then examined by a computer program to see how closely it could be matched to these templates.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1986

The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure.

Predictions of the structures of the antigen-binding domains of an antibody, recorded before its experimental structure determination and tested subsequently, were based on comparative analysis of known antibody structures or on conformational energy calculations. The framework, the relative positions of the hypervariable regions, and the folds of four of the hypervariable loops were predicted correctly. This portion includes all residues in contact with the antigen, in this case hen egg white lysozyme, implying that the main chain conformation of the antibody combining site does not change upon ligation. The conformations of three residues in each of the other two hypervariable loops are different in the predicted models and the experimental structure.

Amino Acid Sequence↗
PubMed1986

The relation between the divergence of sequence and structure in proteins.

Homologous proteins have regions which retain the same general fold and regions where the folds differ. For pairs of distantly related proteins (residue identity approximately 20%), the regions with the same fold may comprise less than half of each molecule. The regions with the same general fold differ in structure by amounts that increase as the amino acid sequences diverge. The root mean square deviation in the positions of the main chain atoms, delta, is related to the fraction of mutated residues, H, by the expression: delta(A) = 0.40 e1.87H.

Amino Acid Sequence↗
PubMed1985

Domain association in immunoglobulin molecules. The packing of variable domains.

We have analyzed the structure of the interface between VL and VH domains in three immunoglobulin fragments: Fab KOL, Fab NEW and Fab MCPC 603. About 1800 A2 of protein surface is buried between the domains. Approximately three quarters of this interface is formed by the packing of the VL and VH beta-sheets in the conserved "framework" and one quarter from contacts between the hypervariable regions. The beta-sheets that form the interface have edge strands that are strongly twisted (coiled) by beta-bulges. As a result, the edge strands fold back over their own beta-sheet at two diagonally opposite corners. When the VL and VH domains pack together, residues from these edge strands form the central part of the interface and give what we call a three-layer packing; i.e. there is a third layer composed of side-chains inserted between the two backbone side-chain layers that are usually in contact. This three-layer packing is different from previously described beta-sheet packings. The 12 residues that form the central part of the three observed VL-VH packings are absolutely or very strongly conserved in all immunoglobulin sequences. This strongly suggests that the structure described here is a general model for the association of VL and VH domains and that the three-layer packing plays a central role in forming the antibody combining site.

Amino Acid Sequence↗
PubMed1985

Haemoglobin: the surface buried between the alpha 1 beta 1 and alpha 2 beta 2 dimers in the deoxy and oxy structures.

Using the newly available refined co-ordinates of deoxy and oxyhaemoglobin, we have re-examined and compared the interfaces between the dimers alpha 1 beta 1 and alpha 2 beta 2. The most extensive monomer-monomer contacts are between alpha 1 and beta 2, and, symmetrically, alpha 2 and beta 1. In oxyhaemoglobin these interfaces bury 700 A2 less protein surface than in deoxyhaemoglobin. The alpha 1 alpha 2 interface involves similar salt bridges in both forms, but in oxyhaemoglobin buries 240 A2 more surface than in deoxyhaemoglobin. There is a loosely packed beta 1 beta 2 interface burying 320 A2 of surface in oxyhaemoglobin; there is no beta 1 beta 2 interface in deoxyhaemoglobin. The greater stability of the deoxy form, in the absence of ligands, can be attributed to a combination of hydrophobic, van der Waals' and electrostatic interactions.

Amino Acid Sequence↗
PubMed1985

Helix movements and the reconstruction of the haem pocket during the evolution of the cytochrome c family.

Analysis of cytochromes c (tuna), c2 (Rhodospirillum rubrum), c550 (Paracoccus denitrificans) and c551 (Pseudomonas aeruginosa) shows that they contain 48 residues identifiable as homologous from superposition of the structures. The other 34 to 64 residues are in loops that vary greatly in sequence, length and conformation, or in alpha-helices that are found in only some of the structures. Of the 48 homologous residues, 17 are in three segments which pack onto the haem faces. In all four structures, these segments have the same conformations, and the same locations relative to the haem. The other 31 residues are in three alpha-helices which are in contact with each other. These form the back and one side of the haem pocket. In cytochrome c551 the positions of the three alpha-helices have shifted and rotated, in comparison with cytochromes c and c2, by up to 5 A and 25 degrees relative to the haem. These shifts, facilitated by mutations at the helix-helix interfaces, are related to the reconstruction of the propionic acid side of the haem pocket described by Almassy & Dickerson (1978). Together these effects produce alternative structures for the haem pocket. This mechanism of adaptation to mutation contrasts with that observed in the globins. In the globins, mutations also produce changes in helix interfaces and shifts of packed helices, but in the globins these shifts are coupled to conserve the structure of the haem pocket.

Animals↗
PubMed1984

Mechanisms of domain closure in proteins.

Certain enzymes respond to the binding of substrates and coenzymes by the closure of an active site that lies in a cleft between two domains. We have examined the mechanism of the domain closure in citrate synthase, for which atomic co-ordinates are available for "open" and "closed" forms. We show that the mechanism of domain closure involves small shifts and rotations of packed helices within the two domains and at their interface. Large motions of distant segments of the structure are the cumulative effect of the small relative shifts in intervening pairs of packed segments. These shifts are accommodated not by changes in packing but rather by small conformational changes in side-chains. We call this the helix interface shear mechanism of domain closure. The relative movements of packed helices follow the principles suggested by our recent study of insulin. This mechanism of domain closure is quite different from the hinge mechanisms that allow the rigid body movements of domains in immunoglobulins. The large interface between the domains of citrate synthase precludes a simple hinge mechanism for its conformational change. The helix interface shear mechanism of conformational change occurs in other enzymes that contain extensive domain-domain interfaces.

Alcohol Dehydrogenase↗
PubMed1983

Transmission of conformational change in insulin.

Crystal structures of insulin contain molecules that are similar but not identical in conformation. Packed helices move relative to each other, these shifts being accommodated by motions of side-chain atoms arising from small changes in torsion angles. Such low-energy conformational adjustments can accommodate shifts of no more than approximately 1.5 A. This limits the extent to which conformational changes can be dissipated locally, causing their transmission over long distances.

Allosteric Regulation↗