Dihedral angle

About: Dihedral angle is a research topic. Over the lifetime, 15718 publications have been published within this topic receiving 174904 citations.

Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: A Lac Repressor Headpiece Structure Based on Information on J‐coupling and from Presence and Absence of NOE's

Abstract: In recent years a procedure has been developed by which the three-dimensional (3D) structure of biomolecules can be derived from 2D NMR data. This procedure combines model building with restrained energy minimization (EM) and molecular dynamics (MD) techniques. Distance information from NOE's is incorporated in the form of an upper limit distance restraining term that is added to the interatomic potential function. Here, two improvements of the refinement procedure are introduced. First, the information that is contained in empty parts of 2D-NOE spectra is transformed into, so-called, non-NOE's which are modelled by adding a lower limit distance restraining term to the potential function for each non-NOE proton pair. Secondly, the information that is contained in the occurrence of large J-coupling constants for specific dihedrals is modelled by adding a sinusoidal dihedral angle restraining term to the potential function for each dihedral angle with a large J-value. The improved refinement procedure is tested by application of the lac repressor headpiece. Both the inclusion of non-NOE data and the inclusion of J-coupling information markedly improve the result of the restrained MD refinement of headpiece. In the refinement procedure MD simulation is used for searching configuration space. Energy barriers which are too high to be crossed by MD are surmounted by manually changing the model structures on a picture system. The resulting close non-bonded contacts are relaxed by EM. The final structure of headpiece satisfies essentially all 169 NOE and 9529 non-NOE distance constraints as well as the 6Cα – Cβ dihedral angle values corresponding to the measured J-coupling values.

A comprehensive study of the rotational energy profiles of organic systems by ab initio MO theory, forming a basis for peptide torsional parameters

Abstract: Ab initio molecular orbital calculations have been carried out on over 50 model organic molecules and ions to provide the data necessary in the determination of torsional parameters for a force field involving polypeptides. The rotational energy profiles were obtained at the HF/6-31G*//HF/6-31G* level. The results were supported, in many cases, by full geometry optimizations and with consideration of correlation corrections at the MP2 level. With the exception of the dihedral angle being studied, all of the molecules were fully optimized with C1 symmetry. © 1995 by John Wiley & Sons, Inc.

Three-dimensional structure of phoratoxin in solution: combined use of nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

Abstract: The solution conformation of phoratoxin, a 46-residue plant protein, has been investigated by /sup 1/H nuclear magnetic resonance (NMR) spectroscopy. The spectrum is assigned in a sequential manner by a combination of two-dimensional NMR techniques to demonstrate through-bond and through-space (< 5 A) connectivities. A set of 331 approximate interproton distance restraints and six phi backbone torsion angle restraints is derived from the two-dimensional nuclear Overhauser enhancement and double quantum filtered homonuclear correlated spectra, respectively. These restraints are used as the basis of a structure determination with a metric matrix distance geometry algorithm. A total of eight structures are computed in this manner and subjected to refinement by restrained molecular dynamics in which the experimental restraints are incorporated into the total energy function of the system in the form of square well effective potentials. The overall shape of phoratoxin is that of the capital letter L, similar to that of crambin and ..cap alpha../sub 1/-purothionin, with the longer arm comprising two ..cap alpha..-helices at an angle of approx. 140/sup 0/ to each other and the shorter arm a mini-antiparallel ..beta..-sheet and a loop made up of two turns and a strand.

Preferred Conformation of C-Lactose at the Free and Peanut Lectin Bound States

Abstract: A conformational analysis of methyl -C-lactoside (5) is carried out (Table 1), which suggests the preferred solution conformation of 5 to be described as a mixture of conformers A ( = 300; = 60) and B ( = 300; = 300) to a first approximation. Applying a modified Karplus equation for the vicinal coupling constants observed for the H.a and H.1' protons of 5, the dihedral angle ( = O.5'-C.1'-C.a-C.4) was deduced to be approximately +280. Nuclear Overhauser effect (NOE) experiments were then conducted on 5-D2 and its parent methyl -O-lactoside in a 7:3 mixture of pyridine-d5 and methanol-d4, qualitatively demonstrating that the conformational characteristics of both methyl -C- and -O-lactosides at the free states are represented as a mixture of two conformers A and B, but their relative population may be different. Through X-ray analysis, it has been definitively established that the conformation ( = 297(7) and = 120(2)) of C-lactose bound to peanut lectin is practically identical to the conformation ( = 291(6) and = 118(9)) of its parent O-lactose bound to the same protein.