Characterizing the inherent flexibility of a protein provides an important link between structure and function. In this article, we examine some of the methods used to determine protein flexibility, and address several unanswered questions relating to them. We perform 4 ns simulations of bovine pancreatic trypsin inhibitor !BPTI" in solution and in a crystal. For comparison, we also calculate a...

Protein conformational changes play a critical role in biological functions such as ligand-protein and protein-protein interactions. Due to the noise in structural data, determining salient conformational changes reliably and efficiently is a challenging problem. This paper presents an efficient algorithm for analyzing protein conformational changes, when the data is noisy. It applies a statist...

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The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence...

Techniques from graph theory are applied to analyze the bond networks in proteins and identify the flexible and rigid regions. The bond network consists of distance constraints defined by the covalent and hydrogen bonds and salt bridges in the protein, identified by geometric and energetic criteria. We use an algorithm that counts the degrees of freedom within this constraint network and that i...

Biomolecular motors are tiny engines that transport material at the microscopic level within biological cells. Since biomolecular motors typically transport cargo that are much larger than themselves, one would expect the speed of such a motor to be severely limited by the small diffusion coefficient of its enormous cargo. It has been suggested by Berg and Kahn [Mobility and Recognition in Cell...

This lecture talked about two examples of using FIRST to explore protein flexibility: ROCK [1, 2] and FRODA [3]. 1 The ROCK Algorithm 1.1 Terminology Ring: A closed loop of bonds in which any two atoms are connected by two distinct paths. Interlocked rings: Two rings that share common bond(s). Ring cluster: A collection of rings that are interlocked with one another. Side branches: All atoms th...

This work shows how to decrease the complexity of modeling flexibility in proteins by reducing the number of dimensions necessary to model important macromolecular motions such as the induced-fit process. Induced fit occurs during the binding of a protein to other proteins, nucleic acids, or small molecules (ligands) and is a critical part of protein function. It is now widely accepted that con...

quency motions, the so called "essential" degrees of freedom [1, 2], which typically appear in timescales of nanoseconds to microseconds and play important roles in signalling, activation and enzyme function. Despite the rapid growth of computer power these timescales are not accessible with current molecular dynamic simulations systems. The CONCOORD system attempts to alleviate this sampling p...

Normal mode analysis (NMA) is a standard technique for studying the dynamics of biological systems. It provides an analytic description of the dynamics in a macromolecular system near a minimum by using a harmonic approximation of the potential. NMA can be applied in the analysis of protein flexibility. It has been shown that over half of the 3800 Yale protein movements can be modelled in a str...