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Biomedical subjects

A S Kolaskar

Publications and source records attributed to A S Kolaskar.

34 records · Page 2Linked to original sources
PubMed1988

Prediction of the recognition sites on 16S and 23S rRNAs from E. coli for the formation of 16S-23S rRNA complex.

Interactions between RNA molecules have been postulated to play an important role in the assembly of ribosomes. Using the sequence analysis and the search of continuous complementary regions on 16S rRNA and 23S rRNA, the recognition sites involved in the formation of ribosome of E. coli are postulated. The number of postulated sites was narrowed down by taking available experimental data. The suggestive evidence for correct postulation is obtained from sequence comparison studies of 16S and 23S rRNAs from various species. The sites 891-899 and 1195-1203 on 16S rRNA along with the corresponding complementary sites 1904-1912 and 760-768 on 23S rRNA are predicted to be the most probable candidates for the sites of recognition between 16S and 23S rRNAs. The possibility of the involvement of the additional site 630-638 on 16S rRNA with its complementary site 2031-2039 on 23S rRNA cannot be ruled out.

Computer Simulation↗
PubMed1986

Contextual constraints on codon pair usage: structural and biological implications.

Complementary DNA sequence data of 278 protein coding genes from prokaryotic systems have been analysed at the level of near neighbour codon pairs. Our analysis points out that constraints exist even at the level of near neighbour codon pairs. These constraints are in addition to those which arise due to relative levels of tRNA. Codon pairs, which in the data base have different occurrence values from their expected values, neither have common secondary structure nor do have better stabilization due to high base stacking. Our study points out that there are strong interaction between constituent codons in these codon pairs. These strongly interacting codon pairs, we suggest, are involved in the formation of three dimensional structural elements of cDNA/mRNA and interact with ribosome and thus modulate translation.

Base Sequence↗
PubMed1986

Analysis of repeating oligonucleotide sequences in ribonucleic acids using an Apple II microcomputer.

A simple computer program has been developed to locate repeating subsequences of all possible lengths in a given nucleic acid. The observed number of repeats of subsequences was compared with the expected number of such repeats in several RNAs. The analysis showed that, in the case of rRNAs, there are no constraints in the choice of the fourth and the higher order nucleotides, while the selection is maximum at the level of nearest neighbour. This is, however, not true for RNAs coding for proteins, where the constraints are also found at the level of nucleotides containing five or more bases.

Algorithms↗
PubMed1985

A method to locate protein coding sequences in DNA of prokaryotic systems.

cDNA sequence data from E. coli phages, for which complete genome sequences are known, have been analysed, From this analysis thirteen triplets have been identified as markers to distinguish protein-coding frames from fortuitous open reading frames. The region of -18 to +18 nucleotides around ATG/GTG, has been analysed and used to identify initiator codons from internal ATG/GTG. With the aid of criteria defined above a method has been developed to locate protein coding sequences by a combination of 'gene search by signal' and 'gene search by content' approaches. Application of this method to prokaryotic systems including those which were not part of our data base indicates that it is quite accurate and general in nature.

Bacterial Proteins↗
PubMed1983

Conformational properties of pairs of amino acids.

Crystal structure data of 31 different globular proteins were analysed. Potentials for all 400 pairs of 20 amino acid residues in helix, extended structure, chain reversals and coil state were obtained. Analysis of these potentials showed that tripeptides of amino acid residues are not linear combinations of amino acids. The association effect of these tripeptides depends on the types of amino acids associated, the position of amino acids in the pair and the secondary structure in which the pair exists. This built-in information in tripeptides should be used in polypeptide and protein folding studies.

Amino Acids↗
PubMed1982

Obligatory amino acids in primitive proteins.

Conformational similarity among amino acid residues, a property derived by analysing (phi, psi)-probability distributions of 20 proteinous amino acids from 38 different globular proteins, is used to arrive at a set of six 'obligatory' amino acids of primitive proteins. The amino acids Ser, Val, Leu, Asp, Gly and Pro have been argued to be 'obligatory' and to represent, conformationally, the remaining amino acids. The reasons for consideration of these six residues as 'obligatory' are discussed. Methods to check the validity of our proposition are suggested.

Amino Acid Sequence↗
PubMed1982

Side chain characteristic main chain conformations of amino acid residues.

Main chain conformation characteristics of the respective side chains of the 20 naturally occurring amino acid residues were obtained by the analysis of (phi, psi)-data from the crystal structures of 38 different globular proteins. The following observations are of interest: (i) For amino acids other than Glu, Thr and aliphatic amino acids, at least one main chain conformation is stabilised solely by side chain atoms. Such conformations are listed. (ii) In globular proteins, the main chain conformations which are significantly destabilised by side chain atom interactions are observed. The stabilising force for those conformations seems to come from main chain atom interactions. (iii) A set of conformations for which the main chain and side chain interactions are almost equal but in opposite directions, is listed and these conformations will be taken by residues mainly due to the effect of surroundings. The results can be used to study the folding of polypeptide chains and they also provide an insight into the role of the respective side chains on main chin conformations of amino acid residues.

Amino Acids↗
PubMed1980

Reversals of polypeptide chain in globular proteins.

A simple algorithm has been developed to detect beta-bends and 'loops'-chain reversals containing five amino acid residues, using only coordinates of C alpha-atoms from crystal structure data of globular proteins using the above algorithm. Analysis of bends have showed that the total number of bends in each protein (TB) is linearly related to total number of non-hydrophobic residues in that protein which in turn is related linearly to total number of amino acid residues. Secondly, we found that a large number of consecutive bends occur in each protein which give rise to on an average only three independent residues per turn. Positional preference of amino acid residues in chain reversals is stressed. Consideration of pairs of amino acid residues in positions (i + 1) and (i + 2) of bends seems to provide a more reliable basis for predicting chain reversals in proteins.

Amino Acids↗
PubMed1979

Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Amino Acid Sequence↗
PubMedDate not supplied

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools.

A B-cell epitope is the three-dimensional structure within an antigen that can be bound to the variable region of an antibody. The prediction of B-cell epitopes is highly desirable for various immunological applications, but has presented a set of unique challenges to the bioinformatics and immunology communities. Improving the accuracy of B-cell epitope prediction methods depends on a community consensus on the data and metrics utilized to develop and evaluate such tools. A workshop, sponsored by the National Institute of Allergy and Infectious Disease (NIAID), was recently held in Washington, DC to discuss the current state of the B-cell epitope prediction field. Many of the currently available tools were surveyed and a set of recommendations was devised to facilitate improvements in the currently existing tools and to expedite future tool development. An underlying theme of the recommendations put forth by the panel is increased collaboration among research groups. By developing common datasets, standardized data formats, and the means with which to consolidate information, we hope to greatly enhance the development of B-cell epitope prediction tools.

Animals↗
PubMedDate not supplied

Recognition of helper T cell epitopes in envelope (E) glycoprotein of Japanese encephalitis, west Nile and Dengue viruses.

Helper T (Th) cell antigenic sites were predicted from the primary amino acid sequence (approximately 500 in length) of the envelope (E) glycoprotein (gp) of Japanese encephalitis (JE), West Nile (WN) and Dengue (DEN) I-IV flaviviruses. Prediction of Th epitopes was done by analyzing the occurrence of amphipathic segments, Rothbard-Taylor tetra/pentamer motifs and presence of alpha helix-preferring amino acids. The simultaneous occurrence of all these parameters in segments of E gp were used as criteria for prediction as Th epitopes. Only one cross reactive epitope was predicted in the C-terminal region of the E gp predicted segments of all flaviviruses analyzed. This region is one of the longest amphipathic stretch (approximately from 420 to 455) and also has a fairly large amphipathic score. Based on the predicted findings three selected peptides were synthesized and analyzed for their ability to induce in vitro T cell proliferative response in different inbred strains of mice (Balb/c, C57BL6, C3H/HeJ). Synthetic peptide I and II prepared from C-terminal region gave a cross reactive response to JE, WN and Den-II in Balb/c and C3H/HeJ mice. Synthetic peptide III prepared from N-terminal region gave a proliferative response to DEN-II in Balb/c strain only, indicating differential antigen presentation.

Algorithms↗
PubMedDate not supplied

Prediction of conformational states of amino acids using a Ramachandran plot.

(phi, psi) data from crystal structures of 221 proteins having high resolution and sequence similarity cut-off at the 25% level were analysed by dividing the Ramachandran plot in three regions representing three conformational states: (i) conformational state 1: conformations in the (phi, psi) range from (-140 degrees, -100 degrees) to (0 degrees, 0 degrees); (ii) conformational state 2: conformations with (phi, psi) from (-180 degrees, 80 degrees) to (0 degrees, 180 degrees); and (iii) conformational state 3: all the remaining conformations in the (phi, psi) plane which are not included in the above two conformational states. Normalized probability values of the occurrence of single amino acid residues in conformational regions 1-3 and similar values for dipeptides were calculated. Comparisons of single residue and dipeptide normalized probability values have shown that short-range interactions, although strong, destabilize conformational states of only 44 dipeptides out of the 400 x 9 possible states. However, dipeptide frequency values provide better resolving power than single-residue potentials when used to predict conformational states of residues in a protein from its primary structure. The simple approach used in the present study to predict conformational states yields an accuracy of > 70% for 14 proteins and an accuracy in the range of 50-70% for 247 proteins. Thus these studies point out yet another use of the Ramachandran plot and the role of tertiary interactions in protein folding.

Algorithms↗