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Biomedical subjects

M Prabhakaran

Publications and source records attributed to M Prabhakaran.

At least 37 records · Page 2Linked to original sources
PubMed1989

Tooth enamel protein, amelogenin, has a probable beta-spiral internal channel, Gln112-Leu138, within a single polypeptide chain: preliminary molecular mechanics and dynamics studies.

Molecular dynamics simulation, with backbone constraints for 20 ps of equilibration and simulation, of a repeating polypeptide segment, Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-Met-(Gln-Pro-Leu )4, constituting residues 112-138 of bovine amelolgenin, a 19.35 kD hydrophobic protein, are discussed. It is generally believed that the above polypeptide segment is important for the interaction of amelogenin with Ca++ ions, which occurs in the early phases of enamel mineralization. An energetically stable structure of the above polypeptide with recurrent beta-turns is observed and contains a pore of approximately 1 A radius along the helical that can accommodate an unhydrated Ca++ ion. The length of the polypeptide possesses correct dimensions to span a bilayer. The proposed structure is unique among known polypeptide and protein structures.

Amelogenin↗
PubMed1989

Identification of peptide hormones of the amphipathic helix class using the helical hydrophobic moment algorithm.

Eisenberg's helical hydrophobic moment (less than mu H greater than) algorithm was applied to the analysis of the primary structure of amphipathic alpha-helical peptide hormones and an optimal method for identifying other peptides of this class determined. We quantitate and compare known amphipathic helical peptide hormones with a second group of peptides with proven nonamphipathic properties and determine the best method of distinguishing between them. The respective means of the maximum 11 residue less than mu H greater than for the amphipathic helical and control peptides were 0.46 (+/-/-0.07) and 0.33 (0.07) (P + 0.004). To better reflect the amphipathic potential of the entire peptide, the percent of 11 residue segments in each peptide above a particular less than mu H greater than was plotted vs less than mu H greater than. The resulting curves are referred to as HM-C. The mean HM-C (of the two groups) was highly significantly different such that the HM-C method was superior to others in its ability to distinguish amphipathic from nonamphipathic peptides. Several potential new members of this structural class were identified using this approach. Molecular modeling of a portion of one of these, prolactin inhibitory factor, reveals a strongly amphipathic alpha helix at residues 4-21. This computer-based method may enable rapid identification of peptides of the amphipathic alpha-helix class.

Algorithms↗
PubMed1989

Secondary structure and limited three-dimensional structure of bovine amelogenin.

Secondary structural features of bovine amelogenin, a hydrophobic protein of developing enamel implicated in ename mineralization, are derived using 2D NMR spectroscopy in solution and molecular mechanics-dynamics studies. A beta-turn: beta-sheet model with some "unordered" segments was previously proposed from circular dichroism, Fourier-transform infrared and Raman spectroscopy augmented by Chou-Fasman predictive algorithm. The proposed structure contains a repetitive beta-turn segment, "beta-spiral" between Gln112 and Leu138 residues containing a (Pro, Leu, Gln) rich segment. The beta-spiral structure offers a probable site for interaction of Ca++ ions. Assignment of proton resonances using 2D COSY spectroscopy is presently in progress. Preliminary 2D NOESY spectra have revealed the presence of Tyr residues (TRAP segment) on the surface of amelogenin molecule and clusters of cross peaks reminiscent of beta-turns and sheets which are consistent with the primary structure and proposed secondary structures of amelogenin. The channel-like beta-spiral structure embedded in amelogenin provides a novel mechanism for trapping of Ca++ ions and their passage for a hydrophobic protein sparse in Ser(P) and charged amino acid residues.

Amelogenin↗
PubMed1988

AUGUR: a program to predict, display and analyze the tertiary structure of B-DNA.

AUGUR is a program to predict, display and analyze the three-dimensional structure of B-DNA. The user can choose one of six models to predict the helical parameters of a given sequence. These parameters are then used to generate the coordinates of the DNA model in three-dimensional space (trajectory). The trajectory can be displayed and rotated on a graphics terminal. The trajectory and helical parameters can also be searched for bends and structural homologues.

Computer Graphics↗
PubMed1985

Atomic motions in phenylalanine transfer RNA probed by molecular dynamics simulations.

A 24 psec molecular dynamics simulation of tRNAPhe reveals a very stable model whose average structure is close to that of the crystallographic studies. The root mean square atomic motions correlate very well with the thermal factors from crystallography and are largely determined by packing forces. These motions are generally more anisotropic than those seen in a molecular dynamics simulation of a globular protein, and the anisotropic effects are also primarily a consequence of packing considerations. The development and examination of molecular dynamics models for macromolecules is an interesting basic research problem in biophysical chemistry, and it is now reasonably well advanced. The more exciting tasks of using these models to predict experimental properties and to examine biological function are just beginning.

Models, Molecular↗
PubMed1984

Phenylalanine transfer RNA: molecular dynamics simulation.

Yeast phenylalanine transfer RNA was subjected to a 12-picosecond molecular dynamics simulation. The principal features of the x-ray crystallographic analysis are reproduced, and the amplitudes of atomic displacements appear to be determined by the degree of exposure of the atoms. An analysis of the hydrogen bonds shows a correlation between the average length of a bond and the fluctuation in that length and reveals a rocking motion of bases in Watson-Crick guanine X cytosine base pairs. The in-plane motions of the bases are generally of larger amplitude than the out-of-plane motions, and there are correlations in the motions of adjacent bases.

Chemical Phenomena↗
PubMed1984

Spatial constraints and group behaviour in globular proteins.

A comparative analysis has been attempted on the spatial placement of amino acid residues derived from radial, ellipsoidal and exposure arrangements. The group behaviour of residues and their restraining influence in protein folding have been brought out. A study is also made on the geometry of proteins, the exposure arrangement of residues and the spatial distribution of the physical properties of the residues in globular proteins. It has been shown that the group constraints along with the information on the shape of the globular proteins would be highly useful in assigning the spatial and exposure arrangements of residues in globular proteins.

Amino Acids↗
PubMed1983

Molecular dynamics of phenylalanine transfer RNA.

The atomic motions of yeast phenylalanine transfer RNA have been simulated using the molecular dynamics algorithm. Two simulations were carried out for a period of 12 picoseconds, one with a normal Van der Waals potential and the other with a modified Van der Waals potential intended to mimic the effect of solvent. An analysis of large scale motions, surface exposure, root mean square displacements, helical oscillations and relaxation mechanisms reveals the maintenance of stability in the simulated structures and the general similarity of the various dynamic features of the two simulations. The regions of conformational flexibility and rigidity for tRNA(Phe) have been shown in a quantitative measure through this approach.

Computer Simulation↗
PubMed1980

Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins.

Amino acid residues acquire characteristic hydrophobic environments in globular proteins. Using the crystal data on 21 proteins, a new scale of hydrophobic indices for the residues is set up. This scale provides valuable information with regard to hydrophobic domains, nucleation sites, surface domains, loop sites and the spatial positions of residues in protein molecules.

Amino Acids↗