AJ Rader

An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is the first step towards understanding molecular mechanisms relevant to biological functions.

Background Endoglucanases are usually considered to be synergistically involved in the initial stages of cellulose breakdown-an essential step in the bioprocessing of lignocellulosic plant materials into bioethanol. Despite their economic importance, we currently lack a basic understanding of how some endoglucanases can sustain their ability to function at elevated temperatures required for bioprocessing, while others cannot.

The term, physics, is derived from the Greek word, physike, meaning the science of nature. This leaves little outside the realm of possible study for a physicist. The field of biophysics represents a set of topics that share the methodology of studying biological processes with perspective from underlying physical properties. Although the idea of applying techniques and theories from physics to problems of biological significance is not new, biophysics as a field is still in the development stage with many significant, unresolved questions.

Similarities between different protein structures have led to the identification of protein families based upon some measure of structural similarity. Using these similarities one can classify proteins into structural families and higher-order groupings from which inferred function can be transferred. When taken for a large number of proteins, these schemes point to evolutionary relationships between organisms. We propose a novel classification scheme based upon the structurally-inspired dynamics of each protein.

Abstract In this article we review how constraint theory can be applied to proteins to give useful information about the rigid and flexible regions. This approach includes all the constraints in a biomolecule that are important at room temperature. A rigid region decomposition determines the rigid regions (both stressed and unstressed) and the flexible regions that separate them.

The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.

The acquired-immunodeficiency syndrome has evolved into a major worldwide epidemic. Significant effort has been made in the development of antiviral therapies. A new strategy for vaccine and drug design that complements the existing cocktail therapy is to target entry of the human immunodeficiency virus (HIV). Such an approach provides the advantage of interfering with multiple intermediates in this multi-step process. The extraordinary conformational flexibility, glycosylation, and strain variations of viral glycoprotein gp120 cause general viral evasion of humoral immune response and thus complicate the development of an effective vaccine. Especially difficult to define are the conformation of gp120 before CD4 engagement as well as the relative orientations of the V1/V2 and V3 loops with respect to the inner and outer domains. In this study, we used Floppy Inclusion and Rigid Substructure Topography (FIRST), a program based on graph theory, to analyze the flexibility and rigidity of all known HIV-1 gp120 structures. A flexibility index is used to describe and compare the spatial distribution of protein flexibility and rigidity of these structures in isolation and in complex with CD4, CD4-mimics, and neutralizing antibodies. Using this flexibility analysis, we identified a universal rigid region (the alpha2 helix) as well as the consensus largest rigid cluster involving a beta-sheet located on the coreceptor binding face. Both of these regions may serve as stable targets for vaccine design and drug discovery. Detailed comparisons of the changes in flexibility based on strain variations, stabilizing mutations, binding features of CD4 mimics, and impact of b12 binding are reported.

An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards understanding molecular mechanisms relevant to biological function. We present a web-based system, oGNM that enables users to calculate online the shape and dispersion of normal modes of motion for proteins, oligonucleotides and their complexes, or associated biological units, using the Gaussian Network Model (GNM). Computations with the new engine are 5–6 orders of magnitude faster than those using conventional normal mode analyses. Two cases studies illustrate the utility of oGNM. The first shows that the thermal fluctuations predicted for 1250 non-homologous proteins correlate well with X-ray crystallographic data over a broad range [7.3–15 Å] of inter-residue interaction cutoff distances and the correlations improve with increasing observation temperatures. The second study, focused on 64 oligonucleotides and oligonucleotide–protein complexes, shows that good agreement with experiments is achieved by representing each nucleotide by three GNM nodes (as opposed to one-node-per-residue in proteins) along with uniform interaction ranges for all components of the complexes. These results open the way to a rapid assessment of the dynamics of DNA/RNA-containing complexes. The server can be accessed at http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm.