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 analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.
Abstract: A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibitor in the full conformational space of the molecule (1,740 degrees of freedom); that is, all bond lengths and angles, as well as dihedral angles, are included for the 580-atom system consisting of all heavy atoms and polar hydrogens. The heavy-atom frequency spectrum shows a dense distribution between 3 and 1,800 cm-1, with 350 modes below 216 cm-1. Most of the low-frequency modes, of which many have significant anharmonic character, are found to be delocalized over the protein. The root-mean-square amplitudes of the atomic fluctuations are calculated at 300 K from the normal modes and compared with those obtained from a solution molecular dynamics simulation based on the same potential function; very good agreement is obtained for the variation in the main-chain fluctuations as a function of residue number, though larger differences occur for the side chains. The fluctuations are generally, though not always, dominated by frequencies below 30 cm-1, in accord with the results of the dynamics simulation. The vibrational contributions to the thermodynamic properties of the protein are calculated as a function of temperature; the effects of perturbations on the spectrum, suggested for ligand or substrate binding, are examined. The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.
790 citations
TL;DR: A molecular-dynamics calculation on a hydrated protein, crambin, demonstrates that neighboring dihedral angles are correlated to local transitions in the protein backbone, and that the amplitude of collective excitations, representing correlated global motions in theprotein, samples multicentered distributions.
Abstract: A molecular-dynamics calculation on a hydrated protein, crambin, demonstrates that (i) neighboring dihedral angles are correlated to local transitions in the protein backbone, and that (ii) the amplitude of collective excitations, representing correlated global motions in the protein, samples multicentered distributions. The time dependence of the multicentered dihedral and collective excitations show rapid transitions from the center of one distribution to another, followed for some time by damped, low-amplitude motions around one center. The global nonlinear collective excitations are responsible for most of the atomic fluctuations of the molecule. An analysis appropriate to multimodal conformations is reported.
763 citations
TL;DR: Configurations that are rare for exposed residues are even rarer for buried residues, suggesting that, while the folded structure puts little strain on side-chain conformations, the side- chain positions with the lowest energy in the unfolded structure are chosen preferentially during folding.
759 citations
TL;DR: In this article, the authors explored the topological characteristics of multidimensional potential energy surfaces and mapped the full conformation space on the set of local minima, which is used to express the temporal behavior of the system in terms of basin-to-basin kinetics.
Abstract: Topological characteristics of multidimensional potential energy surfaces are explored and the full conformation space is mapped on the set of local minima. This map partitions conformation space into energy-dependent or temperature-dependent “attraction basins’’ and generates a “disconnectivity’’ graph that reflects the basin connectivity and characterizes the shape of the multidimensional surface. The partitioning of the conformation space is used to express the temporal behavior of the system in terms of basin-to-basin kinetics instead of the usual state-to-state transitions. For this purpose the transition matrix of the system is expressed in terms of basin-to-basin transitions and the corresponding master equation is solved. As an example, the approach is applied to the tetrapeptide, isobutyryl-(ala)3-NH-methyl (IAN), which is the shortest peptide that can form a full helical turn. A nearly complete list of minima and barriers is available for this system from the work of Czerminiski and Elber. The multidimensional potential energy surface of the peptide is shown to exhibit an overall “funnel’’ shape. The relation between connectivity and spatial proximity in dihedral angle space is examined. It is found that, although the two are similar, closeness in one does not always imply closeness in the other. The basin to basin kinetics is examined using a master equation and the results are interpreted in terms of kinetic connectivity. The conformation space of the peptide is divided up in terms of the surface topography to model its “folding’’ behavior. Even in this very simple system, the kinetics exhibit a “trapping’’ state which appears as a “kinetic intermediate,’’ as in the folding of proteins. The approach described here can be used more generally to classify multidimensional potential energy surfaces and the time development of complex systems.
753 citations
TL;DR: The theory is compared with all the available crystallographic data on simple (di- and tri-) peptides, cyclic peptide, polypeptide and protein structures, and the observed data fully support the conclusions from theory.
696 citations