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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(More)
The realization that experimentally observed functional motions of proteins can be predicted by coarse-grained normal mode analysis has renewed interest in applications to structural biology. Notable applications include the prediction of biologically relevant motions of proteins and supramolecular structures driven by their structure-encoded collective(More)
The motions of large systems such as the ribosome are not fully accessible with conventional molecular simulations. A coarse-grained, less-than-atomic-detail model such as the anisotropic network model (ANM) is a convenient informative tool to study the cooperative motions of the ribosome. The motions of the small 30S subunit, the larger 50S subunit, and(More)
We relate the unfolding of a protein to its loss of structural stability or rigidity. Rigidity and flexibility are well defined concepts in mathematics and physics, with a body of theorems and algorithms that have been applied successfully to materials, allowing the constraints in a network to be related to its deformability. Here we simulate the weakening(More)
MOTIVATION The knowledge of protein structure is not sufficient for understanding and controlling its function. Function is a dynamic property. Although protein structural information has been rapidly accumulating in databases, little effort has been invested to date toward systematically characterizing protein dynamics. The recent success of analytical(More)
With advances in structure genomics, it is now recognized that knowledge of structure alone is insufficient to understand and control the mechanisms of biomolecular function. Additional information in the form of dynamics is needed. As demonstrated in a large number of studies, the machinery of proteins and their complexes can be understood to a good(More)
The unfolding of a protein can be described as a transition from a predominantly rigid, folded structure to an ensemble of denatured states. During unfolding, the hydrogen bonds and salt bridges break, destabilizing the secondary and tertiary structure. Our previous work shows that the network of covalent bonds, salt bridges, hydrogen bonds, and hydrophobic(More)
Peripheral neuropathy can be a devastating complication of diabetes mellitus. This article describes surgical decompression as a means of restoring sensation and relieving painful neuropathy symptoms. A prospective study was performed involving patients diagnosed as having type 1 or type 2 diabetes with lower-extremity peripheral neuropathy. The neuropathy(More)
A new approach is presented for determining the rigid regions in proteins and the flexible joints between them. The short-range forces in proteins are modeled as constraints and we use a recently developed formalism from graph theory to analyze flexibility in the bond network. Forces included in the analysis are the covalent bond-stretching and bond-bending(More)