Saraswathi Vishveshwara

Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and native RNase A

RNase A has been extensively used as a model protein in several biophysical and biochemical studies. Using the available structural and biochemical results, RNase A‐UpA interaction has been computationally modeled at an atomic level. In this study, the molecular dynamics (MD) simulations of native and UpA bound RNase A have been carried out. The gross dynamical behavior and atomic fluctuations of the free and UpA bound RNase A have been characterized. Principal component analysis is carried out to identify the important modes of collective motion and to analyze the changes brought out in these modes of RNase A upon UpA binding. The hydrogen bonds are monitored to study the atomic details of RNase A‐UpA interactions and RNase A‐water interactions. Based on these analysis, the stability of the free and UpA bound RNase A are discussed.

Classification of polymer structures by graph theory

Compact polymers such as proteins obtain their unique conformation by appropriate nonbonded interactions among their monomer residues. Innumerable nonnative compact conformations are also possible, and it is essential to distinguish the native from the nonnative conformations. Toward this goal we have used graph-theoretic methods to classify polymer structures formed by noncovalent interactions. All compact structures on a

Structure-Based Design of Model Proteins

4 times 4

Comparison of the Dynamics of Bovine and Human Angiogenin: A Molecular Dynamics Study

two dimensional lattice and a few conformations on

Determinants of backbone packing in globular proteins: An analysis of spatial neighbours

3 times 3 times 3

Modeling of angiogenin - 3-NMP complex.

cubic lattice have been investigated. The 69 compact conformations in

Threonine mutations in proline helix II of bacteriorhodopsin: a molecular dynamics study

4 times 4

Identification of side-chain clusters in protein structures by a graph spectral method

two dimensional lattice are classified into 12 groups based on the highest eigenvalue and eigenvector. The complex graphs obtained for polymers in a

Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies

3 times 3 times 3

Cell Dynamics of Model Proteins.

lattice space are analyzed. Their eigenvalues and eigenvector components are correlated with the branching structure and the center of the graph. The method has application in classifying real polymers such as proteins into their substructures, cluster, and domains.