Articles written in Journal of Biosciences
Volume 6 Issue 4 October 1984 pp 357-377
Although globular proteins are endowed with well defined three-dimensional structures, they exhibit substantial mobility within the framework of the given three-dimensional structure. The different types of mobility found in proteins by and large correspond to the different levels of organisational hierarchy in protein architecture. They are of considerable structural and functional significance, and can be broadly classified into (a) thermal and conformational fluctuations, (b) segmental mobility, (c) interdomain mobility and (d) intersubunit mobility. Protein crystallographic studies has provided a wealth of information on all of them. The temperature factors derived from X-ray diffraction studies provide a measure of atomic displacements caused by thermal and conformational fluctuations. The variation of displacement along the polypeptide chain have provided functionally significant information on the flexibility of different regions of the molecule in proteins such as myoglobin, lysozyme and prealbumin. Segmental mobility often involves the movement of a region or a segment of a molecule with respect to the rest, as in the transition between the apo and the holo structures of lactate dehydrogenase. It may also involve rigidification of a disordered region of the molecule as in the activation of the zymogens of serine proteases. Transitions between the apo and the holo structures of alcohol dehydrogenase, and between the free and the sugar bound forms of hexokinase, are good examples of interdomain mobility caused by hinge-bending. The capability of different domains to move semi-independently contributes greatly to the versatility of immunoglobulin molecules. Interdomain mobility in citrate synthase appears to be more complex and its study has led to an alternative description of domain closure. The classical and the most thoroughly studied case of intersubunit mobility is that in haemoglobin. The stereochemical mechanism of the action of this allosteric protein clearly brings out the functional subtilities that could be achieved through intersubunit movements. In addition to ligand binding and activation, environmental changes also often cause structural transformations. The reversible transformation between 2 Zn insulin and 4 Zn insulin is caused by changes in the ionic strength of the medium. Adenylate Kinase provides a good example for functionally significant reversible conformational transitions induced by variation in pH. Available evidences indicate that reversible structural transformations in proteins could also be caused by changes in the aqueous environment, including those in the amount of water surrounding protein molecules.
Volume 8 Issue 1-2 August 1985 pp 37-44
Recent experiments in this laboratory on structural transformations caused by controlled dehydration of protein crystals have been reviewed. X-ray diffraction patterns of the following crystals have been examined under varying conditions of environmental humidity in the relative humidity range of 100-75%: a new crystal form of bovine pancreatic ribonuclease A grown from acetone solution in tris buffer (I), the well-known monoclinic form of the protein grown from aqueous ethanol (II), the same form grown from a solution of 2-methyl pentan-2,4-diol in phosphate buffer (III), tetragonal (IV), orthorhombic (V), monoclinic (VI) and triclinic (VII) hen egg white lysozyme, porcine 2 Zn insulin (VIII), porcine 4 Zn insulin (IX) and the crystals of concanavalin A(X). I, II, IV, V and VI undergo one or more transformations as evidenced by discontinuous changes in the unit cell dimensions, the diffraction pattern and the solvent content. Such water-mediated transformations do not appear to occur in the remaining crystals in the relative humidity range explored. The relative humidity at which the transformation occurs is reduced when 2-methyl pentan-2,4-diol is present in the mother liquor. The transformations are affected by the crystal structure but not by the amount of solvent in the crystals. The X-ray investigations reviewed here and other related investigations emphasize the probable importance of water-mediated transformations in exploring hydration of proteins and conformational transitions in them.
Volume 12 Issue 1 March 1987 pp 13-21
A new form of L-histidine L-aspartate monohydrate crystallizes in space group P22 with
Volume 14 Issue 2 June 1989 pp 111-125
X-ray studies on crystalline complexes involving amino acids and peptides: Part XVIII. Crystal structure of a new form of L-arginine D-glutamate and a comparative study of amino acid crystal structures containing molecules of the same and mixed chirality
The new form of L-arginine D-glutamate is monoclinic, P21, with
Volume 20 Issue 2 June 1995 pp 225-234
The crystal structures of the complexes of L and DL histidine with formic acid have been determined as part of an effort to define biologically and evolutionarily important interactions and aggregation patterns. In terms of ionization state and stoichiometry they may be described as L-histidine formate formic acid and DL-histidine formate monohydrate respectively. In the L-histidine complex, amino acid molecules arranged in head-to-tail sequences centred around 21 screw axes are interconnected by formic acid molecules and formate ions. Histidine-formate interactions in the structure gives rise to a characteristic interaction pattern involving a linear array of alternating imidazole groups and formate ions. In DL-histidine formale monohydrate, head-to-tail sequences involving glide related molecules are interconnected through main chain-side chain interactions leading to amino acid layers. The layers are held together by formate ions and water molecules arranged in strings along which the ion and the molecule alternate. The patterns of amino acid aggregation in histidine complexes exhibit considerably higher variability than those in complexes involving arginine and lysine do.
Volume 24 Issue S1 March 1999 pp 33-198
Volume 32 Issue 6 September 2007 pp 1059-1066 Perspectives
Volume 32 Issue 6 September 2007 pp 1089-1110 Articles
The 𝛽-prism II fold lectins of known structure, all from monocots, invariably have three carbohydrate-binding sites in each subunit/domain. Until recently, 𝛽-prism I fold lectins of known structure were all from dicots and they exhibited one carbohydrate-binding site per subunit/domain. However, the recently determined structure of the 𝛽-prism fold I lectin from banana, a monocot, has two very similar carbohydrate-binding sites. This prompted a detailed analysis of all the sequences appropriate for two-lectin folds and which carry one or more relevant carbohydrate-binding motifs. The very recent observation of a 𝛽-prism I fold lectin, griffithsin, with three binding sites in each domain further confirmed the need for such an analysis. The analysis demonstrates substantial diversity in the number of binding sites unrelated to the taxonomical position of the plant source. However, the number of binding sites and the symmetry within the sequence exhibit reasonable correlation. The distribution of the two families of 𝛽-prism fold lectins among plants and the number of binding sites in them, appear to suggest that both of them arose through successive gene duplication, fusion and divergent evolution of the same primitive carbohydrate-binding motif involving a Greek key. Analysis with sequences in individual Greek keys as independent units lends further support to this conclusion. It would seem that the preponderance of three carbohydrate-binding sites per domain in monocot lectins, particularly those with the 𝛽-prism II fold, is related to the role of plant lectins in defence.
Volume 37 Issue 6 December 2012 pp 953-963 Articles
The discrepancy between the X-ray and NMR structures of
Volume 38 Issue 5 December 2013 pp 845-855 Articles
Internal mobility of the two domain molecule of ribosome recycling factor (RRF) is known to be important for its action.
Volume 40 Issue 1 March 2015 pp 13-30 Articles
Structures of crystals of
Volume 40 Issue 5 December 2015 pp 929-941 Articles
The structures of nine independent crystals of bitter gourd seed lectin (BGSL), a non-toxic homologue of type II RIPS, and its sugar complexes have been determined. The four-chain, two-fold symmetric, protein is made up of two identical two-chain modules, each consisting of a catalytic chain and a lectin chain, connected by a disulphide bridge. The lectin chain is made up of two domains. Each domain carries a carbohydrate binding site in type II RIPS of known structure. BGSL has a sugar binding site only on one domain, thus impairing its interaction at the cell surface. The adenine binding site in the catalytic chain is defective. Thus, defects in sugar binding as well as adenine binding appear to contribute to the non-toxicity of the lectin. The plasticity of the molecule is mainly caused by the presence of two possible well defined conformations of a surface loop in the lectin chain. One of them is chosen in the sugar complexes, in a case of conformational selection, as the chosen conformation facilitates an additional interaction with the sugar, involving an arginyl residue in the loop. The 𝑁-glycosylation of the lectin involves a plant-specific glycan while that in toxic type H RIPS of known structure involves a glycan which is animal as well as plant specific.
Volume 44 | Issue 5
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