The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations

2010 ◽  
Vol 500 (1) ◽  
pp. 37-44 ◽  
Author(s):  
Pietro Vidossich ◽  
Mercedes Alfonso-Prieto ◽  
Xavi Carpena ◽  
Ignacio Fita ◽  
Peter C. Loewen ◽  
...  
Keyword(s):  
Ab Initio ◽  
Md Simulations ◽  
X Ray ◽  
X Ray Crystallography ◽  
Distal Side ◽  
Ab Initio Md

scholarly journals The influence of exocyclic lone pairs on the bonding and geometry of type A mesoionic rings

2021 ◽  
Author(s):  
Christopher Antony Ramsden ◽  
Wojciech Piotr Oziminski
Keyword(s):  
Ab Initio ◽  
Type A ◽  
Nbo Analysis ◽  
Ring Systems ◽  
X Ray ◽  
X Ray Crystallography ◽  
Bond Model ◽  
Lone Pairs ◽  
Mp2 Calculations ◽  
Good Agreement

AbstractBased on structures determined by X-ray crystallography, ab initio MP2 calculations on type A mesoionic rings give geometries in good agreement with observed values. A study of four mesoionic ring systems, each with exocyclic oxygen, nitrogen or carbon groups, shows that the presence and configuration of exocyclic lone pairs significantly influences the geometry and configurational preference. Using a localised bond model and NBO analysis, these effects are rationalised in terms of an anomeric interaction of lone pairs with the antibonding orbitals of adjacent σ bonds. In agreement with experiment, similar effects are calculated for pyran-2-imines.

scholarly journals Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations

2014 ◽  
Vol 16 (32) ◽  
pp. 17196-17205 ◽  
Author(s):  
Siv G. Aalbergsjø ◽  
Ewald Pauwels ◽  
Andy Van Yperen-De Deyne ◽  
Veronique Van Speybroeck ◽  
Einar Sagstuen
Keyword(s):  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Md Simulations ◽  
Radical Species ◽  
Automated Generation ◽  
Ab Initio Md

Stabilization of radical products is connected to charge transfer along hydrogen bonds.

The multiple dissociation constants of glutathione disulfide: interpreting experimental pH-titration curves with ab initio MD simulations

2019 ◽  
Vol 21 (18) ◽  
pp. 9212-9217 ◽  
Author(s):  
Vaishali Arunachalam ◽  
Anil Kumar Tummanapelli ◽  
Sukumaran Vasudevan
Keyword(s):  
Complex Systems ◽  
Ab Initio ◽  
Dissociation Constants ◽  
Md Simulations ◽  
Glutathione Disulfide ◽  
Ph Titration ◽  
Titration Curves ◽  
Ab Initio Md

Dissociation constants calculated from ab initio MD simulations can aid the interpretation of the pH-titration curves of complex systems.

scholarly journals Probing the Role of Divalent Metal Ions in a Bacterial Psychrophilic Metalloprotease: Binding Studies of an Enzyme in the Crystalline State by X-Ray Crystallography

2003 ◽  
Vol 185 (14) ◽  
pp. 4195-4203 ◽  
Author(s):  
Stephanie Ravaud ◽  
Patrice Gouet ◽  
Richard Haser ◽  
Nushin Aghajari
Keyword(s):  
Metal Ions ◽  
Calcium Ions ◽  
Calcium Ion ◽  
Crystalline State ◽  
Zinc Ion ◽  
Binding Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Catalytic Zinc

ABSTRACT The psychrophilic alkaline metalloprotease (PAP) produced by a Pseudomonas bacterium isolated in Antarctica belongs to the clan of metzincins, for which a zinc ion is essential for catalytic activity. Binding studies in the crystalline state have been performed by X-ray crystallography in order to improve the understanding of the role of the zinc and calcium ions bound to this protease. Cocrystallization and soaking experiments with EDTA in a concentration range from 1 to 85 mM have resulted in five three-dimensional structures with a distinct number of metal ions occupying the ion-binding sites. Evolution of the structural changes observed in the vicinity of each cation-binding site has been studied as a function of the concentration of EDTA, as well as of time, in the presence of the chelator. Among others, we have found that the catalytic zinc ion was the first ion to be chelated, ahead of a weakly bound calcium ion (Ca 700) exclusive to the psychrophilic enzyme. Upon removal of the catalytic zinc ion, the side chains of the active-site residues His-173, His-179 and Tyr-209 shifted ∼4, 1.0, and 1.6 Å, respectively. Our studies confirm and also explain the sensitivity of PAP toward moderate EDTA concentrations and propose distinct roles for the calcium ions. A new crystal form of native PAP validates our previous predictions regarding the adaptation of this enzyme to cold environments as well as the proteolytic domain calcium ion being exclusive for PAP independent of crystallization conditions.

A comparative study of 2,4-quinazolinediones by X-ray crystallography. The role of the OMe group on the hydrogen bonding motifs formation

2012 ◽  
Vol 11 (4) ◽  
pp. 259-265
Author(s):  
Leticia Guerrero ◽  
Ruben Montalvo ◽  
Ignacio A. Rivero ◽  
Victor Barba
Keyword(s):  
Hydrogen Bonding ◽  
Comparative Study ◽  
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.

Synthesis of N-Urethane-Protected γ-Amino-Functionalized Butenoates and Tautomeric Studies by Means of NMR, X-ray Crystallography and ab initio Calculations

2001 ◽  
Vol 2001 (22) ◽  
pp. 4337 ◽  
Author(s):  
Anastasia Detsi ◽  
Efstathios Gavrielatos ◽  
Marion-Alexandra Adam ◽  
Olga Igglessi-Markopoulou ◽  
John Markopoulos ◽  
...  
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
X Ray ◽  
X Ray Crystallography

Estimation of The Critical Radius for The Nucleation of the C54 Phase in C49 TiSi2: Role of The Difference in Density

1999 ◽  
Vol 580 ◽  
Author(s):  
D.B. Migas ◽  
M. Iannuzzi ◽  
Leo Miglio ◽  
F. La Via ◽  
M.G. Grimaldi
Keyword(s):  
Ab Initio ◽  
Elastic Strain ◽  
Critical Radius ◽  
Lattice Parameters ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Difference ◽  
Two Phases ◽  
The One

AbstractWe discuss the rather scattered measurements of the lattice parameters for C49 TiSi2, which are reported in literature, along with new and accurate X-ray diffraction measurements and ab-initio calculations. Both agree in indicating that the density of the metastable C49 structure cannot be much smaller than the one for the polymorphic C54 phase, as it is commonly reported. We conclude by demonstrating that only in the case of such a smaller difference in density between the two phases, the elastic strain contribution to the nucleation energy of the C54 structure in the C49 matrix can be neglected. The estimation of the critical radius strongly depends on this issue.

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