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

Lu, Mingyang; Ma, Jianpeng

doi:10.1016/j.jmb.2012.12.026

Cited by 6 publications

(8 citation statements)

References 80 publications

(60 reference statements)

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“…Alternative techniques, such as the phaseintegrated method (PIM), which derives anisotropic B factors from low-frequency normal modes (Chen et al, 2010), may significantly improve the biochemical accuracy of modeling efforts. In PIM, the fit between the model and experiment is significantly improved by calculating normal modes in the context of the asymmetric unit rather than individual molecules (Lu & Ma, 2013).…”

Section: Discussionmentioning

confidence: 99%

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

Benschoten

Afonine

Terwilliger

et al. 2015

Acta Crystallogr D Biol Crystallogr

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Section: Discussionmentioning

confidence: 99%

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

Benschoten

Afonine

Terwilliger

et al. 2015

Acta Crystallogr D Biol Crystallogr

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show abstract

“…Alternative techniques, such as the Phase Integrated Method (PIM), which derives anisotropic B factors from low-frequency normal modes (Chen et al , 2010), may significantly improve the biochemical accuracy of modeling efforts. In PIM, the fit between model and experiment is significantly improved by calculating normal modes in the context of the asymmetric unit rather than individual molecules (Lu & Ma, 2013).…”

Section: Discussionmentioning

confidence: 99%

Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

Benschoten

Afonine

Terwilliger

et al. 2015

Preprint

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Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. While Bragg diffraction describes the average positional distribution of crystalline atoms, many different models can fit this distribution equally well. Diffuse X-ray scattering can reduce this degeneracy by directly reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to Translation-Libration-Screw (TLS) refinement, which models rigid body displacement for segments of the macromolecule. To enable calculation of diffuse scattering from TLS refined structures, phenix.tls_models builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how X-ray diffuse scattering can extend macromolecular structural refinement, validation, and analysis. Synopsis A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different Translation-Libration-Screw refinement strategies produce unique diffuse intensity patterns.

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“…For example, the fluctuations of protein in a crystalline environment have been studied in CCS (Hinsen 2008;Riccardi et al 2009;Hafner and Zheng 2010;Lu and Ma 2013). In contrast to these studies, we explored a simple model where the atoms surrounding the relevant molecules in the crystal are considered as a rigid body.…”

Section: Dihedral Angle Systemmentioning

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

Cited by 6 publications

References 80 publications

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

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

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