Optimization of the energy constant of the methionine Sδ—C∊bond forX-PLORrefinement of protein structure

2001 ◽  
Vol 34 (1) ◽  
pp. 80-81 ◽  
Author(s):  
Mamiko Odoko ◽  
Min Yao ◽  
Eiki Yamashita ◽  
Ryosuke Nakashima ◽  
Kunio Hirata ◽  
...  
Keyword(s):  
New York ◽  
Protein Structure ◽  
Bond Energy ◽  
Structure Refinement ◽  
Energy Parameter ◽  
New York University ◽  
Energy Constant ◽  
X Ray ◽  
Bond Lengths ◽  
X Ray Crystallography

The bond energy constant of methionine Sδ—C∊, 170.066 kcal mol−1 Å−2, is given as a default value in X-ray protein structure refinement withX-PLOR[Brünger (1992).X-PLOR Version 3.1. A system for X-ray Crystallography and NMR. New York University Press]. When the atomic parameters of 3564 amino acid residues of bovine heart cytochromecoxidase were refined at 2.0 Å resolution by usingX-PLORwith default restraining parameters, 36 bond lengths deviated by over 0.06 Å from their ideal values. Out of the 36 bonds, 25 were methionine Sδ—C∊bonds. Refinement with an energy parameter of 500.0 kcal mol−1 Å−2for the methionine Sδ—C∊bond resulted in convergence of the Sδ—C∊bond lengths to within 0.06 Å from their ideal values and reduced the crystallographicRand free-Rfactors by 0.6 and 0.3%, respectively. Consequently, a strong bond energy constant for Sδ—C∊of 500.0 kcal mol−1 Å−2is recommended instead of the default value of 170.066 kcal mol−1 Å−2.

scholarly journals A defined structural unit enables de novo design of small-molecule–binding proteins

Science ◽  
2020 ◽  
Vol 369 (6508) ◽  
pp. 1227-1233 ◽  
Author(s):  
Nicholas F. Polizzi ◽  
William F. DeGrado
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Small Molecules ◽  
Structural Unit ◽  
De Novo ◽  
Computational Design ◽  
De Novo Design ◽  
X Ray ◽  
X Ray Crystallography ◽  
Chemical Groups

The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure—a van der Mer (vdM)—that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug–protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.

Syntheses and Structures of Thorium(IV) Complexes with Bis(diphenylphosphino)ethane Dioxide, Ph2P(O)CH2CH2P(O)Ph2, and Bis(diphenylphosphoryl)amide, [Ph2P(O)NP(O)Ph2]

2000 ◽  
Vol 55 (3-4) ◽  
pp. 285-290 ◽  
Author(s):  
Élida Bonfada ◽  
Ernesto Schulz-Lang ◽  
Renato André Zan ◽  
Ulrich Abram
Keyword(s):  
Dimethyl Sulfoxide ◽  
Coordination Sphere ◽  
Phosphine Oxide ◽  
X Ray ◽  
Bond Lengths ◽  
X Ray Crystallography ◽  
Oxygen Atoms

Abstract The cationic thorium(IV) complexes [Th{Ph2P(O)CH2CH2P(O)Ph2}2(NO3)3]NO3 and [Th{Ph2P(O)NP(O)Ph2}3(dmso)2]NO3 have been synthesized by reactions of Th(NO3)4 · 5H2O with bis(diphenylphosphino)ethane dioxide, Ph2P(O)CH2CH2P(O)Ph2 (L1), or ammonium bis(diphenylphosphoryl)amide, (NH4)[Ph2P(O)NP(O)Ph2] (NH4L2), and subsequent recrystallization from dimethyl sulfoxide. The products have been studied spectroscopically and by X-ray crystallography. The thorium atom is ten-co-ordinate in the [Th(L1)2(NO3)3]+ cation with a coordination sphere which does not match one of the idealized polyhedra for ten-coordination. Th-O bonds have been found in the range between 2.342(3) (phosphine oxide) and 2.599(4) A (nitrate). An eight-coordinate thorium atom is found in the [Th(L2)3(dmso)2]+ cation. The almost ideal square-antiprismatic environment of the metal is occupied by oxygen atoms with Th-0 bond lengths between 2.363(6) and 2.392(11) Å

scholarly journals Measuring and modeling diffuse scattering in protein X-ray crystallography

2016 ◽  
Vol 113 (15) ◽  
pp. 4069-4074 ◽  
Author(s):  
Andrew H. Van Benschoten ◽  
Lin Liu ◽  
Ana Gonzalez ◽  
Aaron S. Brewster ◽  
Nicholas K. Sauter ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Structure Refinement ◽  
Normal Modes ◽  
Coarse Grained ◽  
X Ray Diffraction ◽  
Diffuse Intensity ◽  
X Ray ◽  
Protein Motions ◽  
X Ray Crystallography ◽  
Standard Data

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.

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