Introduction and validation of an invariom database for amino-acid, peptide and protein molecules

Dittrich, Birger; Hübschle, Christian B.; Luger, Peter; Spackman, Mark A.

doi:10.1107/s090744490602899x

Cited by 116 publications

(101 citation statements)

References 36 publications

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“…the C atom in alanine) are nearly the same in all compounds containing this atom (Pichon-Pesme et al, 1995). Based on this principle, several databases of transferable multipole parameters have been developed (PichonPesme et al, 1995(PichonPesme et al, , 2004Volkov et al, 2004;Dittrich et al, 2006;Zarychta et al, 2007;Dominiak et al, 2007Dominiak et al, , 2009Domagała et al, 2012). They offer the possibility of constructing a multipole model of any molecule without the need to refine parameters beyond those of the IAM, i.e.…”

Section: Introductionmentioning

confidence: 99%

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

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Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM;Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-HÁ Á ÁO hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

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Section: Introductionmentioning

confidence: 99%

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

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“…This called for the establishment of data banks containing the parameters of the most important pseudo-atoms, defined with respect to well chosen local coordinate systems. The data banks available at present are ELMAM2 (Domagała & Jelsch, 2008) with pseudo-atoms derived from high-resolution diffraction data, UBDB (Koritsanszky et al, 2002) with pseudo-atoms obtained from single-point calculations, and Invariom (Dittrich et al, 2006) with pseudo-atoms derived from geometry-optimized calculations. These data banks can be used to obtain more precise atomic coordinates and displacement parameters by taking care of the asphericity shifts.…”

Section: Beyond the Free-atom Modelmentioning

confidence: 99%

The success story of crystallographyThis Laue centennial article has also been published inZeitschrift für Kristallographie[Schwarzenbach (2012).Z. Kristallogr.227, 52–62].

Schwarzenbach

2011

Acta Cryst Sect A

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Diffractionists usually place the birth of crystallography in 1912 with the first X-ray diffraction experiment of Friedrich, Knipping and Laue. This discovery propelled the mathematical branch of mineralogy to global importance and enabled crystal structure determination. Knowledge of the geometrical structure of matter at atomic resolution had revolutionary consequences for all branches of the natural sciences: physics, chemistry, biology, earth sciences and material science. It is scarcely possible for a single person in a single article to trace and appropriately value all of these developments. This article presents the limited, subjective view of its author and a limited selection of references. The bulk of the article covers the history of X-ray structure determination from the NaCl structure to aperiodic structures and macromolecular structures. The theoretical foundations were available by 1920. The subsequent success of crystallography was then due to the development of diffraction equipment, the theory of the solution of the phase problem, symmetry theory and computers. The many structures becoming known called for the development of crystal chemistry and of data banks. Diffuse scattering from disordered structures without and with partial long-range order allows determination of short-range order. Neutron and electron scattering and diffraction are also mentioned.

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“…This called for the establishment of data banks containing the parameters of the most important pseudo-atoms, defined with respect to well chosen local coordinate systems. The data banks available at present are ELMAM2 (Domagala & Jelsch, 2008) with pseudo-atoms derived from high-resolution diffraction data, UBDB (Koritsanszky et al, 2002) with pseudo-atoms obtained from single-point calculations, and Invariom (Dittrich et al, 2006) with pseudoatoms derived from geometry-optimized calculations. These data banks can be used to obtain more precise atomic coordinates and displacement parameters by taking care of the asphericity shifts.…”

Section: Beyond the Free-atom Modelmentioning

confidence: 99%

The success story of crystallography

Schwarzenbach¹

2012

Zeitschrift für Kristallographie

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Abstract. Diffractionists usually place the birth of crystallography in 1912 with the first X-ray diffraction experiment of Friedrich, Knipping and Laue. This discovery propelled the mathematical branch of mineralogy to global importance and enabled crystal structure determination. Knowledge of the geometrical structure of matter at atomic resolution had revolutionary consequences for all branches of the natural sciences: physics, chemistry, biology, earth sciences and material science. It is scarcely possible for a single person in a single article to trace and appropriately value all of these developments. This article presents the limited, subjective view of its author and a limited selection of references. The bulk of the article covers the history of X-ray structure determination from the NaCl structure to aperiodic structures and macromolecular structures. The theoretical foundations were available by 1920. The subsequent success of crystallography was then due to the development of diffraction equipment, the theory of the solution of the phase problem, symmetry theory and computers. The many structures becoming known called for the development of crystal chemistry and of data banks. Diffuse scattering from disordered structures without and with partial long-range order allows determination of short-range order. Neutron and electron scattering and diffraction are also mentioned.

show abstract

Introduction and validation of an invariom database for amino-acid, peptide and protein molecules

Cited by 116 publications

References 36 publications

The active site of hen egg-white lysozyme: flexibility and chemical bonding

The active site of hen egg-white lysozyme: flexibility and chemical bonding

The success story of crystallographyThis Laue centennial article has also been published inZeitschrift für Kristallographie[Schwarzenbach (2012).Z. Kristallogr.227, 52–62].

The success story of crystallography

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