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Biomedical subjects

C Ramakrishnan

Publications and source records attributed to C Ramakrishnan.

52 records · Page 3Linked to original sources
PubMed1983

Occurrence of a single helix of the collagen type in globular proteins.

The occurrence of an eight-residue long segment of polypeptide chain in collagen helical conformation has been detected in bacteriochlorophyll a-protein by the application of an algorithm for identifying secondary structures in globular proteins from their alpha-carbon positions. This segment spans residues 277 to 284 of the protein and is the longest known stretch of collagen helix to be observed in globular proteins.

Amino Acid Sequence↗
PubMed1982

Identification of secondary structures in globular proteins--a new algorithm.

A new algorithm has been developed for identifying helices, extended structures, and bends from the positions of the alpha-carbon atoms using the virtual bond approach. The parameters used are two virtual bond angles (delta 1 and delta 2), the virtual dihedral angle (theta), and the distance (D) between the terminal alpha-carbon atoms of the tripeptide. The criteria for classification have been worked out by model building as well as from proteins whose complete secondary structures are known. These criteria are as follows: (i) magnitude of theta less than or equal to 60 degrees and (delta 1 + delta 2) less than or equal to 230 degrees for a bend, (ii) for a helix, successive thetas should not differ by more than 30 degrees, and (iii) for an extended structure, the cumulative deviation of the above parameters should not vary by more than 20% from the ideal extended chain. The method developed has been applied successfully to three proteins wherein the coordinates of alpha-carbon atoms alone are known and a complete mapping of the secondary structures has now been obtained. One interesting observation is that the percentage of residues not taking part in helices, extended structures, and bends is very small--of the order of 4%.

Animals↗
PubMed1981

Studies on hydrogen bonds. Part IV. Proposed working criteria for assessing qualitative strength of hydrogen bonds.

The data obtained in the earlier parts of this series for the donor and acceptor end parameters of N-H...O and O-H...O hydrogen bonds have been utilised to obtain a qualitative working criterion to classify the hydrogen bonds into three categories: "very good" (VG), "moderately good" (MG) and weak (W). The general distribution curves for all the four parameters are found to be nearly of the Gaussian type. Assuming that the VG hydrogen bonds lie between O and +/- 1 sigma, MG hydrogen bonds between +/- 1 sigma and +/- 2 sigma, W hydrogen bonds beyond +/- 2 sigma (where sigma is the standard deviation), suitable cut-off limits for classifying the hydrogen bonds in the three categories have been derived. These limits are used to get VG and MG ranges for the four parameters 1 and theta (at the donor end) and zeta and xi (at the acceptor end). The qualitative strength of a hydrogen bond is decided by the cumulative application of the criteria to all the four parameters. The criterion has been further applied to some practical examples in conformation studies such as alpha-helix and can be used for obtaining suitable location of hydrogen atoms to form good hydrogen bonds. An empirical approach to the energy of hydrogen bonds in the three categories has also been presented.

Chemical Phenomena↗
PubMed1980

Stereochemical studies on cyclic peptides. Part XI. Conformation of cyclic pentapeptides having intramolecular 3 leads to 1 hydrogen bonds.

Conformational analysis of cyclic pentapeptides having two intra-ring 3 leads to 1 hydrogen bonds has been carried out. It is found that the structure can easily be formed with trans planar peptide units without causing significant angular strain at the alpha-carbon atoms. Four different types of conformations designated Types I--IV are possible for the backbone structure. Details of these four types of conformations and also the accommodating possibility of these types for allglycyl and all-alanyl residues are presented. Three of the four types have relatively low energies for glycyl residues whereas the other one has a slightly higher energy. When alanyl residues are introduced at the five alpha-carbon atoms, the types that are energetically favourable depend upon the sequence of isomers. Energy calculations have also been carried out for the combinations of glycyl, L- and D-alanyl residues. The theoretical results are compared with available experimental observations both from solution and solid state studies.

Amino Acid Sequence↗
PubMed1979

Stereochemical studies on cyclic peptides. Part X. Conformational analysis of hydrogen bonded cyclic pentapeptides.

Conformational aspects of 4 leads to 1 hydrogen bonded cyclic pentapeptides are considered in this paper from the point of view of "contact criteria" and potential energy calculations. Three types of such hydrogen bonded conformations, designated A1, A2 and B, are possible, involving some amount of strain on the bond angles. The energy of hydrogen bonded cyclopentaglycyl is somewhat less than that of the five-fold symmetrical conformation. The stereochemical feasibility of introducing L- and D-alanyl resudues in these structures has also been studied and the possible types for different sequences of alanyl residues have been determined. The results are discussed further in the light of the limited data available from crystal structure and nuclear magnetic resonance studies on cyclic pentapeptides.

Amino Acid Sequence↗
PubMed1965

Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units.

The conformation of a polypeptide or protein chain may be specified by stating the orientations of the two linked peptide residues at each alpha carbon atom in the chain, namely the two dihedral angles varphi, varphi' about the single bonds N-alphaC and alphaC-C' from a defined standard conformation. By using certain criteria of minimum contact distances between the various atoms, the allowed anges of (varphi, varphi') have been worked out for three values of the angle N-alphaC-C' (tau), namely 105, 110, and 115 degrees for non-glycyl, and 110 and 115 degrees for glycyl residues. The theory is compared with all the available crystallographic data (up to early 1965) on simple (di- and tri-) peptides, cyclic peptides, polypeptide and protein structures, and the observed data fully support the conclusions from theory. The effect of the gamma carbon atom, in its three possible positions, is also discussed, and is found to alter the outer limits of the allowed region of (varphi, varphi') only slightly. The paper contains exhaustive references to the published data on these structures, using x-ray diffraction.

Crystallography↗