Normal mode analysis of Zika virus

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

doi:10.1016/j.compbiolchem.2018.01.004

Cited by 8 publications

(5 citation statements)

References 43 publications

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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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Section: Normal Mode Analysismentioning

confidence: 99%

Normal Mode Analysis as a Routine Part of a Structural Investigation

2019

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“…If the target system has a symmetric structure composed of repeated subunit structures, we can use symmetry-constrained ENM (SCENM) to analyze full models effectively by using only a repeated subunit structure with connectivity information of neighboring subunits instead of handling all the structural information [ 32 , 39 , 40 ]. The advantage of SCENM is its ability to reflect the crystal packing effect of protein structures with reduced computational cost [ 41 ].…”

Section: Methodsmentioning

confidence: 99%

Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures

Kim

Lee

et al. 2018

IJMS

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In order to incorporate functionalization into synthesized DNA nanostructures, enhance their production yield, and utilize them in various applications, it is necessary to study their physical stabilities and dynamic characteristics. Although simulation-based analysis used for DNA nanostructures provides important clues to explain their self-assembly mechanism, structural function, and intrinsic dynamic characteristics, few studies have focused on the simulation of DNA supramolecular structures due to the structural complexity and high computational cost. Here, we demonstrated the feasibility of using normal mode analysis for relatively complex DNA structures with larger molecular weights, i.e., finite-size DNA 2D rings and 3D buckyball structures. The normal mode analysis was carried out using the mass-weighted chemical elastic network model (MWCENM) and the symmetry-constrained elastic network model (SCENM), both of which are precise and efficient modeling methodologies. MWCENM considers both the weight of the nucleotides and the chemical bonds between atoms, and SCENM can obtain mode shapes of a whole structure by using only a repeated unit and its connectivity with neighboring units. Our results show the intrinsic vibrational features of DNA ring structures, which experience inner/outer circle and bridge motions, as well as DNA buckyball structures having overall breathing and local breathing motions. These could be used as the fundamental basis for designing and constructing more complicated DNA nanostructures.

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“…Application of the method to larger systems was hampered by its computational expense. With advances in computer technology and the development of more efficient algorithms, it has become possible to examine larger structures, including the skeletal ryanodine receptor [21], Ca-ATPase [22], GroEL [23][24][25], the ribosome [26][27][28], the yeast nuclear pore complex [29], and virus capsids [30][31][32]. All these will be examined in more detail in Section 3 below.…”

Section: Normal Mode Analysismentioning

confidence: 99%

Normal Mode Analysis: A Tool for Better Understanding Protein Flexibility and Dynamics with Application to Homology Models

Bauer¹,

Bauerová-Hlinková²

2021

Homology Molecular Modeling - Perspectives and Applications

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Molecular dynamics (MD) and normal mode analysis (NMA) are very useful methods for characterizing various dynamic aspects of biological macromolecules. In comparison to MD, NMA is computationally less expensive which facilitates the quick and systematic investigation of protein flexibility and dynamics even for large proteins and protein complexes, whose structure was obtained experimentally or in silico. In particular, NMA can be used to describe the flexible states adopted by a protein around an equilibrium position. These states have been repeatedly shown to have biological relevance and functional significance. This chapter briefly characterizes NMA and describes the elastic network model, a schematic model of protein shape used to decrease the computational cost of this method. Finally, we will describe the applications of this technique to several large proteins and their complexes as well as its use in enhancing protein homology modeling.

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Normal mode analysis of Zika virus

Cited by 8 publications

References 43 publications

Normal Mode Analysis as a Routine Part of a Structural Investigation

Normal Mode Analysis as a Routine Part of a Structural Investigation

Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures

Normal Mode Analysis: A Tool for Better Understanding Protein Flexibility and Dynamics with Application to Homology Models

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