Dynamic characteristics of a flagellar motor protein analyzed using an elastic network model

Choi, Moon-ki; Jo, Soojin; Lee, Byung Ho; Kim, Min Hyeok; Choi, Jae Boong; Kim, Kyunghoon; Kim, Moon Ki

doi:10.1016/j.jmgm.2017.10.001

Cited by 2 publications

(1 citation statement)

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“…Extension to larger systems was, however, hampered by the computational expense of the method. More recently, thanks to both advances in computer equipment as well as new methods based on simpler models, it has become possible to examine larger structures, including the skeletal ryanodine receptor [42], virus capsids [43,44,45], Ca-ATPase [46], Myosin-II [46,47,48], F1-ATPase [49], GroEL [50,51,52], the ribosome [53,54,55], the C-ring of the bacterial flagellar motor [56], and the yeast nuclear pore complex [57].…”

Section: Normal Mode Analysismentioning

confidence: 99%

Normal Mode Analysis as a Routine Part of a Structural Investigation

2019

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Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.

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