scholarly journals Reaction Mechanism of Glutamate Carboxypeptidase II Revealed by Mutagenesis, X-ray Crystallography, and Computational Methods

Biochemistry ◽  
2009 ◽  
Vol 48 (19) ◽  
pp. 4126-4138 ◽  
Author(s):  
Vojtěch Klusák ◽  
Cyril Bařinka ◽  
Anna Plechanovová ◽  
Petra Mlčochová ◽  
Jan Konvalinka ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Computational Methods ◽  
Glutamate Carboxypeptidase Ii ◽  
X Ray ◽  
X Ray Crystallography ◽  
Glutamate Carboxypeptidase

scholarly journals Reaction Mechanism Based on X-ray Crystallography at Atomic Resolution of Endopolygalacutronase I from Fungus Stereum purpureum

2004 ◽  
Vol 51 (2) ◽  
pp. 161-167 ◽  
Author(s):  
Tetsuya Shimizu ◽  
Toru Nakatsu ◽  
Kazuo Miyairi ◽  
Toshikatsu Okuno ◽  
Hiroaki Kato
Keyword(s):  
Reaction Mechanism ◽  
Atomic Resolution ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals Integrated X-ray crystallography, optical and computational methods in studies of structure and luminescence of new synthesized complexes of lanthanides with ligands derived from 2,6-diformylpyridine

Polyhedron ◽  
2011 ◽  
Vol 30 (5) ◽  
pp. 851-859 ◽  
Author(s):  
Gelson Manzoni de Oliveira ◽  
Aline Machado ◽  
Geraldo Wachholz Gomes ◽  
Jorge H.S.K. Monteiro ◽  
Marian R. Davolos ◽  
...  
Keyword(s):  
Computational Methods ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Diamagnetic cobalt(III)tris(o-ethylxanthate) and nickel(II)bis(o-ethylxanthate)

2017 ◽  
Vol 16 (2) ◽  
pp. 138-146 ◽  
Author(s):  
Filip Varga ◽  
Ján Titiš ◽  
Cyril Rajnák ◽  
Ján Moncoľ ◽  
Roman Boča
Keyword(s):  
Ir Spectroscopy ◽  
Single Crystal ◽  
Computational Methods ◽  
Magnetic Measurements ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ethyl Xanthate

Abstract Diamagnetic [Co(xanth)3] and [Ni(xanth)2] complexes have been prepared by reaction of Co(II) and Ni(II) salts with potassium O-ethyl xanthate (Kxanth). The isolated Co(III) and Ni(II) complexes have been characterized by single-crystal X-ray crystallography, UV-VIS and IR spectroscopy, computational methods, and magnetic measurements.

scholarly journals Principles and characteristics of biological assemblies in experimentally determined protein structures

2019 ◽  
Author(s):  
Qifang Xu ◽  
Roland L. Dunbrack
Keyword(s):  
Physical Properties ◽  
Computational Methods ◽  
Structural Information ◽  
Protein Structures ◽  
Sequence Conservation ◽  
Homologous Proteins ◽  
X Ray ◽  
Biologically Relevant ◽  
X Ray Crystallography

AbstractMore than half of all structures in the PDB are assemblies of two or more proteins, including both homooligomers and heterooligomers. Structural information on these assemblies comes from X-ray crystallography, NMR, and cryo-EM spectroscopy. The correct assembly in an X-ray structure is often ambiguous, and computational methods have been developed to identify the most likely biologically relevant assembly based on physical properties of assemblies and sequence conservation in interfaces. Taking advantage of the large number of structures now available, some of the most recent methods have relied on similarity of interfaces and assemblies across structures of homologous proteins.

scholarly journals Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations

2018 ◽  
Vol 294 (1) ◽  
pp. 20-27 ◽  
Author(s):  
Maryam Molakarimi ◽  
Michael A. Gorman ◽  
Ammar Mohseni ◽  
Zaiddodine Pashandi ◽  
Majid Taghdir ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
X Ray ◽  
X Ray Crystallography ◽  
Bioluminescent Protein

scholarly journals Novel bacterial molybdenum and tungsten enzymes: three-dimensional structure, spectroscopy, and reaction mechanism

2005 ◽  
Vol 386 (10) ◽  
pp. 999-1006 ◽  
Author(s):  
Matthias Boll ◽  
Bernhard Schink ◽  
Albrecht Messerschmidt ◽  
Peter M.H. Kroneck
Keyword(s):  
Reaction Mechanism ◽  
Structural Analysis ◽  
Triple Bond ◽  
Three Dimensional ◽  
Reaction Centers ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Coa Reductase ◽  
Tungsten Enzymes

Abstract The molybdenum enzymes 4-hydroxybenzoyl-CoA reductase and pyrogallol-phloroglucinol transhydroxylase and the tungsten enzyme acetylene hydratase catalyze reductive dehydroxylation reactions, i.e., transhydroxylation between phenolic residues and the addition of water to a triple bond. Such activities are unusual for this class of enzymes, which carry either a mononuclear Mo or W center. Crystallization and subsequent structural analysis by high-resolution X-ray crystallography has helped to resolve the reaction centers of these enzymes to a degree that allows us to understand the interaction of the enzyme and the respective substrate(s) in detail, and to develop a concept for the respective reaction mechanism, at least in two cases.

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