Simulation evidence for experimentally detectable low-temperature vibrational inhomogeneity in a globular protein

Lamy, Anne; Souaille, Marc; Smith, Jeremy C.

doi:10.1002/(sici)1097-0282(199609)39:3<471::aid-bip18>3.0.co;2-e

Cited by 21 publications

(14 citation statements)

References 19 publications

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“…There is no a priori reason why these two potential wells should have anything in common; the eective potential well is expected to contain many local minima that even might dier from each other signi®cantly. However, there is evidence that the local minima are very similar to each other [31], and also, up to a global scaling factor, to the eective potential well describing large-scale motions. The evidence for this latter similarity comes from numerous normal mode studies on proteins which, in spite of being limited to a single local minimum of the potential energy surface, can reproduce experimental information that is clearly related to large-scale motions, such as domain motions or the residue dependence of atomic uctuations, if only a scaling factor is applied to the amplitude of the motions.…”

Section: Eective Potential Wellmentioning

confidence: 97%

Harmonicity in slow protein dynamics

et al. 2000

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Section: Eective Potential Wellmentioning

confidence: 97%

Harmonicity in slow protein dynamics

et al. 2000

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“…At low temperatures, proteins are trapped in multiple minima leading to structural inhomogeneity (Elber and Karplus, 1987;Frauenfelder et al, 1991;Ostermann et al, 2000). This leads to dynamical inhomogeneity reflected in broadening of theoretical neutron and infrared spectra (Lamy et al, 1996). To take this inhomogeneity into account, 20 structures were taken from the 300-K simulation trajectories at regular intervals and were energy minimized to a root mean square energy gradient of Ͻ10 Ϫ7 kcal mol Ϫ1 Å Ϫ1 .…”

Section: Normal Modesmentioning

confidence: 99%

Temperature Dependence of Protein Dynamics: Computer Simulation Analysis of Neutron Scattering Properties

Hayward

Smith

2002

Biophysical Journal

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The temperature dependence of the internal dynamics of an isolated protein, bovine pancreatic trypsin inhibitor, is examined using normal mode analysis and molecular dynamics (MD) simulation. It is found that the protein exhibits marked anharmonic dynamics at temperatures of approximately 100-120 K, as evidenced by departure of the MD-derived average mean square displacement from that of the harmonic model. This activation of anharmonic dynamics is at lower temperatures than previously detected in proteins and is found in the absence of solvent molecules. The simulation data are also used to investigate neutron scattering properties. The effects are determined of instrumental energy resolution and of approximations commonly used to extract mean square displacement data from elastic scattering experiments. Both the presence of a distribution of mean square displacements in the protein and the use of the Gaussian approximation to the dynamic structure factor lead to quantified underestimation of the mean square displacement obtained.

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“…The practical relevance of normal mode analysis therefore seems questionable, because it explores only one specific (and arbitrarily chosen) minimum. Moreover, collective motions at physiological temperatures are not determined by the potential energy surface, but by the potential of mean force expressed as a function of a smaller set of ''slow'' variables, which is a much smoother function.Acomparison of normal modes in several closely spaced local minima of Bovine Pancreatic Trypsin Inhibitor (BPTI) 10 has shown that there is an observable variation of the low-frequency modes, but this variation occurs within a well-defined subspace. Comparisons of low-frequency normal modes and the directions of large-amplitude fluctuations in molecular dynamics simulations indicate clear similarities.…”

Section: Introductionmentioning

confidence: 99%

Analysis of domain motions by approximate normal mode calculations

1998

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The identification of dynamical domains in proteins and the description of the low-frequency domain motions are one of the important applications of numerical simulation techniques. The application of these techniques to large proteins requires a substantial computational effort and therefore cannot be performed routinely, if at all. This article shows how physically motivated approximations permit the calculation of low-frequency normal modes in a few minutes on standard desktop computers. The technique is based on the observation that the low-frequency modes, which describe domain motions, are independent of force field details and can be obtained with simplified mechanical models. These models also provide a useful measure for rigidity in proteins, allowing the identification of quasi-rigid domains. The methods are validated by application to three well-studied proteins, crambin, lysozyme, and ATCase. In addition to being useful techniques for studying domain motions, the success of the approximations provides new insight into the relevance of normal mode calculations and the nature of the potential energy surface of proteins.

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Simulation evidence for experimentally detectable low-temperature vibrational inhomogeneity in a globular protein

Cited by 21 publications

References 19 publications

Harmonicity in slow protein dynamics

Harmonicity in slow protein dynamics

Temperature Dependence of Protein Dynamics: Computer Simulation Analysis of Neutron Scattering Properties

Analysis of domain motions by approximate normal mode calculations

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