Internal Mobility of the Basic Pancreatic Trypsin Inhibitor in Solution: A Comparison of NMR Spin Relaxation Measurements and Molecular Dynamics Simulations

Smith, Pieter E. S.; Schaik, René C. van; Szyperski, Thomas; Wüthrich, Kurt; Gunsteren, Wilfred F. van

doi:10.1006/jmbi.1994.0090

Cited by 73 publications

(62 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, for base carbons (sp 2) a lesser contribution is due to the chemical shift anisotropy (oil-cYi), which has been determined to be 185 ppm for the C6 carbon of a thymine base (Williamson and Boxer, 1988). ~3C T l relaxation times can also be determined from molecular dynamics (MD) simulations and so far t3C T l relaxation times have been calculated for proteins (Balasubramanian et al, 1994;Smith et al, 1995). The overall rotational correlation time of a dinucleoside monophosphate, which is nearly spherical and can therefore be described by a single correlation time, is about 150 ps (Norberg and Nilsson, 1994a).…”

Section: Introductionmentioning

confidence: 99%

Internal mobility of the ologonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations

Norberg

Nilsson

1996

J Biomol NMR

View full text Add to dashboard Cite

In this paper we present longitudinal relaxation times, order parameters and effective correlation times for the base and sugar carbons in both strands of the oglionucleotide duplexes d(TCGCG)2 and d(CGCGCG)2, as calculated from 400 ps molecular dynamics trajectories in aqueous solution. The model-free approach (Lipari and Szabo, 1982) was used to determine the amplitudes and time scales of the internal motion. Comparisons were made with NMR relaxation measurements (Borer et al., 1994). The order parameters could acceptably be reproduced, and the effective correlation times were found to be lower than the experimental estimates. Reasonable T1 relaxation times were obtained in comparison with experiment for the nonterminal nucleosides. The T1 relaxation times were found to depend mainly on the order parameters and overall rotational correlation time.

show abstract

Section: Introductionmentioning

confidence: 99%

Internal mobility of the ologonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations

Norberg

Nilsson

1996

J Biomol NMR

View full text Add to dashboard Cite

show abstract

“…8,9 Briefly, the initial coordinates for BPTI were taken from a nuclear magnetic resonance refined structure. 10 BPTI was simulated in a truncated octahedron of length 5.34 nm using the GROMOS simulation package.…”

Section: Methodsmentioning

confidence: 99%

A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins

Smith¹,

Blatt²,

Pettitt³

1997

Proteins

Self Cite

View full text Add to dashboard Cite

A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four C alpha atoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudodihedral involving four sequential C alpha atoms, as well as the triple scalar product for the vectors describing the orientation of the three intervening peptide groups. The method provides a reduction in dimensionality, from the usual combination of multiple phi,psi pairs to a single pair, yielding valuable information concerning the structure and dynamics of these important elements. The new two-dimensional surface is explored by reference to 63 selected protein crystal structures together with a comparison of model built peptides representing the common secondary structural elements. Dynamical aspects on this new surface are examined using a molecular dynamics trajectory of Basic Pancreatic Trypsin Inhibitor.

show abstract

“…It has been widely studied in both computer simulations 25,26 and experiments, 27,28 making it an excellent test case for the multiple time step Langevin dynamics algorithm. The 1BPI crystal structure from the PDB database was used as the starting point for a simulation, 28 and it was evolved for 5,000 iterations.…”

Section: Bptimentioning

confidence: 99%

Multiple time step diffusive Langevin dynamics for proteins

Eastman

Doniach

1998

Proteins

View full text Add to dashboard Cite

We present an algorithm for simulating the long time scale dynamics of proteins and other macromolecules. Our method applies the concept of multiple time step integration to the diffusive Langevin equation, in which short time scale dynamics are replaced by friction and noise. The macromolecular force field is represented at atomic resolution. Slow motions are modeled by constrained Langevin dynamics with very large time steps, while faster degrees of freedom are kept in local thermal equilibrium. In the limit of a sufficiently large molecule, our algorithm is shown to reduce the CPU time required by two orders of magnitude. We test the algorithm on two systems, alanine dipeptide and bovine pancreatic trypsin inhibitor (BPTI), and find that it accurately calculates a variety of equilibrium and dynamical properties. In the case of BPTI, the CPU time required is reduced by nearly a factor of 60 compared to a conventional, unconstrained Langevin simulation using the same force field.

show abstract

Internal Mobility of the Basic Pancreatic Trypsin Inhibitor in Solution: A Comparison of NMR Spin Relaxation Measurements and Molecular Dynamics Simulations

Cited by 73 publications

References 0 publications

Internal mobility of the ologonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations

Internal mobility of the ologonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations

A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins

Multiple time step diffusive Langevin dynamics for proteins

Contact Info

Product

Resources

About