The hinge-bending mode in lysozyme

McCammon, J. Andrew; Gelin, Bruce R.; Karplus, Martin; Wolynes, Peter G.

doi:10.1038/262325a0

Cited by 355 publications

(224 citation statements)

References 12 publications

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“…solved through x-ray crystallography) and R c is a distance cutoff that specifies which pairs of nodes are interacting. Note that k 4 = 0 corresponds to the widely used elastic network model (ENM) [41][42][43], which has proven useful for quantitatively describing amino acid fluctuations at room temperature [41,42,44,45], as well as for predicting or characterizing large-amplitude functional motions of proteins [46][47][48][49][50] in agreement with all-atom models [51][52][53], paving the way for numerous applications in structural biology [54][55][56][57].…”

Section: Methodsmentioning

confidence: 99%

Long-range energy transfer in proteins

Piazza

Sanejouand

2009

Phys. Biol.

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Proteins are large and complex molecular machines. In order to perform their function, most of them need energy, e.g. either in the form of a photon, as in the case of the visual pigment rhodopsin, or through the breaking of a chemical bond, as in the presence of adenosine triphosphate (ATP). Such energy, in turn, has to be transmitted to specific locations, often several tens ofÅ away from where it is initially released. Here we show, within the framework of a coarse-grained nonlinear network model, that energy in a protein can jump from site to site with high yields, covering in many instances remarkably large distances. Following single-site excitations, few specific sites are targeted, systematically within the stiffest regions. Such energy transfers mark the spontaneous formation of a localized mode of nonlinear origin at the destination site, which acts as an efficient energy-accumulating center. Interestingly, yields are found to be optimum for excitation energies in the range of biologically relevant ones.

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Section: Methodsmentioning

confidence: 99%

Long-range energy transfer in proteins

Piazza

Sanejouand

2009

Phys. Biol.

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“…Lysozyme is a classic protein for NMA as its lowest-frequency mode represents a catalytically important hinge-bending motion. 30,31 Figure 2a shows the tip effect in one of the lowest-frequency modes, the fourth vibrational mode, calculated by the conventional eNMA. 5 The amplitude of motion of a flexible loop at the lower-right corner is abnormally large comparing with the rest of the system.…”

Section: Proteins With Single Polypeptide Chainmentioning

confidence: 99%

A New Method for Coarse-Grained Elastic Normal-Mode Analysis

Poon

2006

J. Chem. Theory Comput.

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In this paper, we report a new method for coarse-grained elastic normal-mode analysis. The purpose is to overcome a long-standing problem in the conventional analysis called the tip effect that makes the motional patterns (eigenvectors) of some low-frequency modes irrational. The new method retains the merits of a conventional method such as not requiring lengthy initial energy minimization, which always distorts structures, and also delivers substantially more accurate lowfrequency modes with no tip effect for proteins of any size. This improvement of modes is crucial for certain types of applications such as structural refinement or normal-mode-based sampling.

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“…McCammon et al (1976) studied the hinge-bending mode in lysozyme on a potential energy surface that was obtained by adiabatic mapping. Normal mode analysis was used extensively to study transitions of allosteric proteins by Go, Perahia, andcoworkers (compare, e.g., Ikura &Go, 1993 andPerahia, 1996).…”

Section: Pki(5-24)mentioning

confidence: 99%

Kinase conformations: A computational study of the effect of ligand binding

Helms

McCammon

1997

Protein Science

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Protein function is often controlled by ligand-induced conformational transitions. Yet, in spite of the increasing number of three-dimensional crystal structures of proteins in different conformations, not much is known about the driving forces of these transitions. As an initial step toward exploring the conformational and energetic landscape of protein kinases by computational methods, intramolecular energies and hydration free energies were calculated for different conformations of the catalytic domain of CAMP-dependent protein kinase (cAPK) with a continuum (Poisson) model for the electrostatics. Three protein kinase crystal structures for ternary complexes of cAPK with the peptide inhibitor PKI(5-24) and ATP or AMP-PNP were modeled into idealized intermediate and open conformations. Concordant with experimental observation, we find that the binding of PKI(5-24) is more effective in stabilizing the closed and intermediate forms of cAPK than ATP. PKI(5-24) seems to drive the final closure of the active site cleft from intermediate to closed state because ATP does not distinguish between these two states. Binding of PKI(5-24) and ATP is energetically additive.

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The hinge-bending mode in lysozyme

Cited by 355 publications

References 12 publications

Long-range energy transfer in proteins

Long-range energy transfer in proteins

A New Method for Coarse-Grained Elastic Normal-Mode Analysis

Kinase conformations: A computational study of the effect of ligand binding

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