Topic
Dihedral angle
About: Dihedral angle is a research topic. Over the lifetime, 15718 publications have been published within this topic receiving 174904 citations.
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TL;DR: The REDAC approach reduces the computation time for obtaining a group of acceptable conformers with the program DIANA 5-100-fold, depending on the complexity of the protein structure, and retains good sampling of conformation space.
Abstract: A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985)J. Mol. Biol.,186, 611) is described, which makes use of redundant dihedral angle constraints (REDAC) derived from preliminary calculations of the complete structure. The REDAC approach reduces the computation time for obtaining a group of acceptable conformers with the program DIANA 5-100-fold, depending on the complexity of the protein structure, and retains good sampling of conformation space.
310 citations
TL;DR: It is suggested that the enhanced stability of thermostable proteins relative to thermolabile ones cannot be attributed to a common determinant such as metal ion or hydrophobic stabilization, but in a given instance may be due to rather subtle differences inhydrophobic character, metal binding, hydrogen bonding, ionic interactions, or a combination of all of these.
306 citations
TL;DR: It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide.
Abstract: It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {phi(n)} to the metric coordinate space {x(n)=cos phi(n),y(n)=sin phi(n)} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300 ns molecular dynamics simulation, a critical comparison of the various methods is given.
302 citations
TL;DR: On the basis of the experience with the structure determination of coagulation factor XIII, an algorithm is developed for the identification of possibly overlooked cis peptide bonds that exploits the deviations of geometrical parameters from ideality.
296 citations
TL;DR: In this paper, an alternative definition of natural internal coordinates is presented, which can be generated for any molecular topology, no matter how complicated, and is fully nonredundant.
Abstract: Following on from the earlier work of Pulay and Fogarasi [J. Chem. Phys. 96, 2856 (1992)] we present an alternative definition of natural internal coordinates. This set of delocalized internal coordinates can be generated for any molecular topology, no matter how complicated, and is fully nonredundant. Using an appropriate Schmidt‐orthogonalization procedure, all standard bond length, bond angle, and dihedral angle constraints can be imposed within our internal coordinate scheme. Combinatorial constraints (in which sums or differences of stretches, bends, and torsions remain constant) can also be imposed. Optimizations on some fairly large systems (50–100 atoms) show that delocalized internal coordinates are far superior to Cartesians even with reliable Hessian information available at the starting geometry.
295 citations