Collective motions in protein structures: Applications of elastic network models built from electron density distributions

Leherte, Laurence; Vercauteren, Daniel P.

doi:10.1016/j.cpc.2008.01.013

Cited by 3 publications

(2 citation statements)

References 35 publications

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“…4 B). Residues 2,9,16,[23][24][25]28,29,39,48,52,53,61,62,74, and 75 also display diversity, albeit to a lesser extent, in the fluctuation direction of the second mode. These residues are also observed to lie along the rotational axes (Fig.…”

Section: Diversity In Orientational Correlationsmentioning

confidence: 99%

“…Recently, elastic network models have gained considerable attention for studying the large-scale motion of protein structures that are relevant to function (25)(26)(27)(28)(29)(30)(31). This suggests that the structures evolved in such a way that the intrinsic elastic low-frequency modes are the most efficient way for the structures to function.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Rationale for More Diverse Inhibitors in Competition with Substrates in HIV-1 Protease

Özer

Schiffer

Haliloğlu

2010

Biophysical Journal

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The structural fluctuations of HIV-1 protease in interaction with its substrates versus inhibitors were analyzed using the anisotropic network model. The directions of fluctuations in the most cooperative functional modes differ mainly around the dynamically key regions, i.e., the hinge axes, which appear to be more flexible in substrate complexes. The flexibility of HIV-1 protease is likely optimized for the substrates' turnover, resulting in substrate complexes being dynamic. In contrast, in an inhibitor complex, the inhibitor should bind and lock down to inactivate the active site. Protease and ligands are not independent. Substrates are also more flexible than inhibitors and have the potential to meet the dynamic distributions that are inherent in the protease. This may suggest a rationale and guidelines for designing inhibitors that can better fit the ensemble of binding sites that are dynamically accessible to the protease.

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