Toward ab initio refinement of protein X-ray crystal structures: interpreting and correlating structural fluctuations

Falklöf, Olle; Collyer, Charles A.; Reimers, Jeffrey R.

doi:10.1007/s00214-011-1076-8

Cited by 8 publications

(6 citation statements)

References 116 publications

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“…Falklöf et al made the important observation that, despite being obtained at very high resolution, only 25% of the residues of 2VB1 are surrounded by a 5 Å region in which the atomic structure is unambiguously defined. 69 Therefore it was advised to only optimize those well-defined regions and to leave the structure unchanged for the other. In our previous study 110 we followed this recommendation and we do the same herein.…”

Section: The Initial Structure and Previous Workmentioning

confidence: 99%

“…For the sake of simplicity we chose the AMBER force-field 136 with B3LYP 76-77 /6-31G* 78 atomic charges taken from the previous studies. 38,69 In preliminary calculations we also explored the possibility of electronic embedding in the ONIOM calculations, i.e. the MM charges directly influence the QM Hamiltonian.…”

Section: Other Computational Detailsmentioning

confidence: 99%

“…Previously some of us have developed methods for construction of such a mapping and applied it to HEWL. 69 This creates an ensemble, shown in Figure 1, of 8 chemically reasonable, fully interconnected, global protein structures that generates the same scattering R factor as the original PDB-deposited uncorrelated structure. We use this structure to investigate QM methods for protein structure optimization and for quantum-refinement.…”

Section: Introductionmentioning

confidence: 99%

“…Schematic depiction of the 2x2x2 supercell of lysozyme 69. Each distinct lysozyme molecule is labeled with letters A-H and contains different conformations.…”

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confidence: 99%

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Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures

2014

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We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G* approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications.

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Section: The Initial Structure and Previous Workmentioning

confidence: 99%

Section: Other Computational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Schematic depiction of the 2x2x2 supercell of lysozyme 69. Each distinct lysozyme molecule is labeled with letters A-H and contains different conformations.…”

mentioning

confidence: 99%

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Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures

2014

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“…An alternative to extending these restraints with additional information is to design better potential functions, which may be not as sophisticated as those used in the molecular simulation field but more tailored to the context of structure refinement. Another approach is the use of QM/MM (quantum mechanics/molecular mechanic) methods to generate accurate structures of small molecules in macromolecular structures or even whole macromolecular structures (Canfield et al, 2006;Reimers, 2011;Falköf, Collyer and Reimers, 2012).…”

Section: Some Current Challenges and Future Goalsmentioning

confidence: 99%

Macromolecular crystallographic estructure refinement

Afonine

Urzhumtsev

Adams

2015

Arbor

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Model refinement is a key step in crystallographic structure determination that ensures final atomic structure of macromolecule represents measured diffraction data as good as possible. Several decades have been put into developing methods and computational tools to streamline this step. In this manuscript we provide a brief overview of major milestones of crystallographic computing and methods development pertinent to structure refinement.KEYWORDS: bulk-solvent; constraints; fast gradient calculation; Fourier maps; maximum-likelihood; minimization; neutrons; optimization; refinement; restraints; structure factors; X-rays. RESUMEN:El refinamiento es un paso clave en el proceso de determinación de una estructura cristalográfica al garantizar que la estructura atómica de la macromolécula final represente de la mejor manera posible los datos de difracción. Han hecho falta varias décadas para poder desarrollar nuevos métodos y herramientas computacionales dirigidas a dinamizar esta etapa. En este artículo ofrecemos un breve resumen de los principales hitos en la computación cristalográfica y de los nuevos métodos relevantes para el refinamiento de estructuras.PALABRAS CLAVE: cálculos rápidos de gradiente; constricciones; factores de estructura; mapas de Fourier; máxima verosimilitud; medio acuoso; minimización; neutrones; optimización; rayos-X; refinamiento; restricciones.

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Computational modeling of extended systems

DiLabio¹

2012

Perspectives on Theoretical Chemistry

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Toward ab initio refinement of protein X-ray crystal structures: interpreting and correlating structural fluctuations

Cited by 8 publications

References 116 publications

Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures

Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures

Macromolecular crystallographic estructure refinement

Computational modeling of extended systems

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