scholarly journals Hydration of Biological Macromolecules: From Small Solutes to Proteins and Nucleic Acids

1996 ◽  
Vol 463 ◽  
Author(s):  
Shekhar Garde ◽  
Gerhard Hummer ◽  
Michael E. Paulaitis ◽  
Angel E. Garcia
Keyword(s):  
Potential Of Mean Force ◽  
Water Molecules ◽  
Biological Macromolecules ◽  
Particle Correlation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Catabolite Activator Protein ◽  
Hydrophobic Solutes ◽  
Small Hydrophobic ◽  
Good Agreement

We present a method that uses two- and three-particle correlation functions between solute atoms and water molecules to approximate the density profile of water surrounding biomolecules. The method is based on a potential of mean force expansion and uses X-ray crystallography, NMR, or modeling structural input information on the biomolecule. For small hydrophobic solutes, we have calculated entropies of hydration using the predicted water densities that are in good agreement with experimental results. We have also predicted the hydration of thecatabolite activator protein-DNAcomplex. The method is extremely efficient and makes possible the study of hydration of large biomolecules within CPU minutes.

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.

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

X-ray Crystallography at High Pressure to Probe Conformational Fluctuations in Biological Macromolecules

2007 ◽  
Author(s):  
Eric Girard ◽  
Richard Kahn ◽  
Anne-Claire Dhaussy ◽  
Isabella Ascone ◽  
Mohamed Mezouar ◽  
...  
Keyword(s):  
High Pressure ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

scholarly journals Molecular Recognition in Proton-Transfer Compounds of Brucine with Achiral Substituted Salicylic Acid Analogues

2006 ◽  
Vol 59 (5) ◽  
pp. 320 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth ◽  
Peter C. Healy ◽  
Jonathan M. White
Keyword(s):  
Proton Transfer ◽  
Three Dimensional ◽  
Water Molecules ◽  
Sulfosalicylic Acid ◽  
X Ray ◽  
X Ray Crystallography ◽  
Guest Species ◽  
Substituted Benzoic Acids ◽  
Proton Transfer Compounds ◽  
Hydrogen Bonded

The 1:1 proton-transfer brucinium compounds from the reaction of the alkaloid brucine with 5-nitrosalicylic acid, 3,5-dinitrosalicylic acid, and 5-sulfosalicylic acid, namely anhydrous brucinium 5-nitrosalicylate (1), brucinium 3,5-dinitrosalicylate monohydrate (2), and brucinium 5-sulfosalicylate trihydrate (3) have been prepared and their crystal structures determined by X-ray crystallography. All structures further demonstrate the selectivity of brucine for meta-substituted benzoic acids and comprise three-dimensional hydrogen-bonded framework polymers. Two of the compounds (1 and 3) have the previously described undulating brucine sheet host-substructures which incorporate interstitially hydrogen-bonded salicylate anion guest species and additionally in 3 the water molecules of solvation. The structure of 2 differs in having a three-centre brucinium–salicylate anion bidentate N+–H···O(carboxyl) hydrogen-bonding association linking the species through interstitial associations involving also the water molecules of solvation. A review of the crystallographic structural literature on strychnine and brucine is also given.

scholarly journals The Resolution in X-ray Crystallography and Single-Particle Cryogenic Electron Microscopy

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 580
Author(s):  
Victor R.A. Dubach ◽  
Albert Guskov
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particle Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Fourier Transform

X-ray crystallography and single-particle analysis cryogenic electron microscopy are essential techniques for uncovering the three-dimensional structures of biological macromolecules. Both techniques rely on the Fourier transform to calculate experimental maps. However, one of the crucial parameters, resolution, is rather broadly defined. Here, the methods to determine the resolution in X-ray crystallography and single-particle analysis are summarized. In X-ray crystallography, it is becoming increasingly more common to include reflections discarded previously by traditionally used standards, allowing for the inclusion of incomplete and anisotropic reflections into the refinement process. In general, the resolution is the smallest lattice spacing given by Bragg’s law for a particular set of X-ray diffraction intensities; however, typically the resolution is truncated by the user during the data processing based on certain parameters and later it is used during refinement. However, at which resolution to perform such a truncation is not always clear and this makes it very confusing for the novices entering the structural biology field. Furthermore, it is argued that the effective resolution should be also reported as it is a more descriptive measure accounting for anisotropy and incompleteness of the data. In single particle cryo-EM, the situation is not much better, as multiple ways exist to determine the resolution, such as Fourier shell correlation, spectral signal-to-noise ratio and the Fourier neighbor correlation. The most widely accepted is the Fourier shell correlation using a threshold of 0.143 to define the resolution (so-called “gold-standard”), although it is still debated whether this is the correct threshold. Besides, the resolution obtained from the Fourier shell correlation is an estimate of varying resolution across the density map. In reality, the interpretability of the map is more important than the numerical value of the resolution.

scholarly journals Temperature-dependent macromolecular X-ray crystallography

2010 ◽  
Vol 66 (4) ◽  
pp. 437-446 ◽  
Author(s):  
Martin Weik ◽  
Jacques-Philippe Colletier
Keyword(s):  
Radiation Damage ◽  
Routine Data ◽  
Dynamical Behaviour ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structural Details ◽  
Induced Changes ◽  
Structural Insights ◽  
Reaction Initiation

X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.

scholarly journals New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences

2017 ◽  
Vol 37 (4) ◽  
Author(s):  
John R. Helliwell
Keyword(s):  
Crystal Structure ◽  
Data Bank ◽  
Crystal Structure Analysis ◽  
Public Understanding ◽  
Biological Macromolecules ◽  
Hydrogen Atoms ◽  
X Ray ◽  
The Public ◽  
X Ray Crystallography ◽  
Chemical Catalysis

Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 ‘small molecule’ crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography’s role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.

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