All-atom modeling of anisotropic atomic fluctuations in protein crystal structures

Hafner, Jeffrey; Zheng, Wenjun

doi:10.1063/1.3646312

Cited by 9 publications

(14 citation statements)

References 49 publications

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“…Consequently, it is clear that inter-AU packing interactions have a large impact on the internal motions of structures in crystalline environment. Our finding is in sharp contrast to what reported in references 69, 79 . It is worth mentioning that it is an approximation that the inter-AU interactions are treated as the packing interactions in crystal.…”

Section: Resultscontrasting

confidence: 99%

PIM: Phase Integrated Method for Normal Mode Analysis of Biomolecules in a Crystalline Environment

2013

Journal of Molecular Biology

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In this study, a normal mode analysis, named phase integrated method (PIM), is developed for computing modes of biomolecules in crystalline environment. PIM can calculate low-frequency modes on one or a few asymmetric units and generate exact modes of a whole unit cell according to space group symmetry, while the translational symmetry between unit cells is maintained via periodic boundary condition. Therefore, the method can dramatically reduce computational cost in mode calculation in the presence of crystal symmetry. PIM also has an option to map modes onto a single asymmetric unit to form an orthonormalized mode set, which can be directly applied to normal-mode-based thermal parameter refinement in X-ray crystallography. The performance of PIM was tested on all 65 space groups available in protein crystals (one protein for each space group) and on another set of 83 ultra-high-resolution X-ray structures. The results showed that considering space group symmetry in mode calculation is crucial for accurately describing vibrational motion in crystalline environment. Moreover, the optimal inter-asymmetric-unit packing stiffness was found to be about 60% of that of intra-asymmetric-unit interactions (nonbonded interaction only).

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Section: Resultscontrasting

confidence: 99%

PIM: Phase Integrated Method for Normal Mode Analysis of Biomolecules in a Crystalline Environment

2013

Journal of Molecular Biology

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“…As temperature factors can only provide information regarding the magnitude of the atomic fluctuations in most of the PDB data, it is generally problematic to compare the calculated and experimentally observed atomic fluctuations with respect to their directional properties. Such a comparison is possible for the PDB data with anisotropic temperature factors, and there is some literature that discusses this method (Atilgan et al 2001;Eyal et al 2007;Yang et al 2009;Hafner and Zheng 2011). However, we have not discussed this in our review.…”

Section: Fluctuation Of Atomsmentioning

confidence: 99%

Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank

Wako

Endo

2017

Biophys Rev

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Normal mode analysis (NMA) can facilitate quick and systematic investigation of protein dynamics using data from the Protein Data Bank (PDB). We developed an elastic network model-based NMA program using dihedral angles as independent variables. Compared to the NMA programs that use Cartesian coordinates as independent variables, key attributes of the proposed program are as follows: (1) chain connectivity related to the folding pattern of a polypeptide chain is naturally embedded in the model; (2) the full-atom system is acceptable, and owing to a considerably smaller number of independent variables, the PDB data can be used without further manipulation; (3) the number of variables can be easily reduced by some of the rotatable dihedral angles; (4) the PDB data for any molecule besides proteins can be considered without coarse-graining; and (5) individual motions of constituent subunits and ligand molecules can be easily decomposed into external and internal motions to examine their mutual and intrinsic motions. Its performance is illustrated with an example of a DNA-binding allosteric protein, a catabolite activator protein. In particular, the focus is on the conformational change upon cAMP and DNA binding, and on the communication between their binding sites remotely located from each other. In this illustration, NMA creates a vivid picture of the protein dynamics at various levels of the structures, i.e., atoms, residues, secondary structures, domains, subunits, and the complete system, including DNA and cAMP. Comparative studies of the specific protein in different states, e.g., apo-and holo-conformations, and free and complexed configurations, provide useful information for studying structurally and functionally important aspects of the protein.

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“…Those calculations included all proteins and waters in the unit cell, and were the first attempts to include crystal contact forces. However, there is some evidence that crystal contact forces are weak 32,46 and as we are interested in the intramolecular motions rather than the lattice phonons, we assume zero-crystal contact forces and calculate the net crystal response by summing the single-molecule response over the unit cell, accounting for the molecular rotations for the crystal symmetry group:…”

Section: Methodsmentioning

confidence: 99%

Optical measurements of long-range protein vibrations

et al. 2014

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Protein biological function depends on structural flexibility and change. From cellular communication through membrane ion channels to oxygen uptake and delivery by haemoglobin, structural changes are critical. It has been suggested that vibrations that extend through the protein play a crucial role in controlling these structural changes. While nature may utilize such long-range vibrations for optimization of biological processes, bench-top characterization of these extended structural motions for engineered biochemistry has been elusive. Here we show the first optical observation of long-range protein vibrational modes. This is achieved by orientation-sensitive terahertz near-field microscopy measurements of chicken egg white lysozyme single crystals. Underdamped modes are found to exist for frequencies 410 cm À 1 . The existence of these persisting motions indicates that damping and intermode coupling are weaker than previously assumed. The methodology developed permits protein engineering based on dynamical network optimization.

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All-atom modeling of anisotropic atomic fluctuations in protein crystal structures

Cited by 9 publications

References 49 publications

PIM: Phase Integrated Method for Normal Mode Analysis of Biomolecules in a Crystalline Environment

PIM: Phase Integrated Method for Normal Mode Analysis of Biomolecules in a Crystalline Environment

Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank

Optical measurements of long-range protein vibrations

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