Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties

AbstractLow-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.

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A distributed lattice of aligned atoms exists in a protein structure: A hierarchical clustering study of displacement parameters in bovine trypsin

10.1101/475889 ◽

2018 ◽

Cited By ~ 1

Author(s):

Viktor Ahlberg Gagnér ◽

Ida Lundholm ◽

Maria-Jose Garcia-Bonete ◽

Helena Rodilla ◽

Ran Friedman ◽

...

Keyword(s):

Protein Structure ◽

Low Frequency ◽

Atomic Displacement ◽

Thz Radiation ◽

Vibrational Dynamics ◽

X Ray Crystallography ◽

Atomic Displacements ◽

Bovine Trypsin ◽

Main Challenge ◽

And Function

AbstractLow-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increases upon terahertz irradiation. Atomic displacement similarities develop between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arise from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. This method can ultimately reveal how the alignment of chemically related atoms and the underlying polar vibrational dynamics make a protein structure stable.

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Local and global analysis of macromolecular atomic displacement parameters

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798320011043 ◽

2020 ◽

Vol 76 (10) ◽

pp. 926-937

Author(s):

Rafiga C. Masmaliyeva ◽

Kave H. Babai ◽

Garib N. Murshudov

Keyword(s):

Global Analysis ◽

Expectation Maximization Algorithm ◽

Atomic Displacement ◽

Local Analysis ◽

X Ray Crystallography ◽

Inverse Gamma ◽

Metal Atoms ◽

Atomic Displacement Parameters ◽

Global And Local ◽

Validation Tool

This paper describes the global and local analysis of atomic displacement parameters (ADPs) of macromolecules in X-ray crystallography. The distribution of ADPs is shown to follow the shifted inverse-gamma distribution or a mixture of these distributions. The mixture parameters are estimated using the expectation–maximization algorithm. In addition, a method for the resolution- and individual ADP-dependent local analysis of neighbouring atoms has been designed. This method facilitates the detection of mismodelled atoms, heavy-metal atoms and disordered and/or incorrectly modelled ligands. Both global and local analyses can be used to detect errors in atomic models, thus helping in the (re)building, refinement and validation of macromolecular structures. This method can also serve as an additional validation tool during PDB deposition.

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Multilayer Diffraction Reveals That Colloidal Superlattices Approach the Structural Perfection of Single Crystals

10.26434/chemrxiv.13103507 ◽

2020 ◽

Author(s):

Stefano Toso ◽

Dmitry Baranov ◽

Davide Altamura ◽

Francesco Scattarella ◽

Jakob Dahl ◽

...

Keyword(s):

Structural Information ◽

Accurate Determination ◽

Diffraction Method ◽

Atomic Displacement ◽

Interparticle Spacing ◽

X Rays ◽

Structural Perfection ◽

Fitting Algorithm ◽

Atomic Displacement Parameters

Colloidal superlattices are fascinating materials made of ordered nanocrystals, yet they are rarely called “atomically precise.” That is unsurprising, given how challenging it is to quantify the degree of structural order in these materials. However, once that order crosses a certain threshold, constructive interference of X-rays diffracted by the nanocrystals dominates the diffraction pattern, offering a wealth of structural information. By treating nanocrystals as scattering sources forming a self-probing interferometer, we developed a multilayer diffraction method that enabled the accurate determination of nanocrystal size, interparticle spacing, and their fluctuations for samples of self-assembled CsPbBr<sub>3</sub> and PbS nanomaterials. The average nanocrystal displacement of 0.32-1.4 Å in the studied superlattices provides a figure of merit for their structural perfection and approaches the atomic displacement parameters found in traditional crystals. The method requires a laboratory-grade diffractometer and an open-source fitting algorithm for data analysis, providing a competitive alternative to resource-intensive synchrotron experiments.

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Exploring ligand dynamics in protein crystal structures with ensemble refinement

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798321006513 ◽

2021 ◽

Vol 77 (8) ◽

Author(s):

Octav Caldararu ◽

Vilhelm Ekberg ◽

Derek T. Logan ◽

Esko Oksanen ◽

Ulf Ryde

Keyword(s):

Crystal Structures ◽

Automatic Generation ◽

Atomic Displacement ◽

Point Of View ◽

Protein Crystal ◽

Statistical Point ◽

X Ray Crystallography ◽

Conformational Diversity ◽

Atomic Displacement Parameters ◽

Dynamics Simulations

Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein–ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein–ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and R free values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.

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Atomic Motion in Crystals from Neutron Diffraction Experiments

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314089050 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1094-C1094

Author(s):

Bryan Chakoumakos

Keyword(s):

Neutron Diffraction ◽

Structural Information ◽

National Laboratory ◽

Atomic Displacement ◽

Department Of Energy ◽

Temperature Dependent ◽

Oak Ridge ◽

Filled Skutterudites ◽

Atomic Displacement Parameters ◽

Physical Phenomena

Static or dynamic disorder in crystals causes a decrease in the Bragg peak intensity, and given sufficient number of Bragg peaks over an extended Q-range, atomic displacement parameters (ADPs) can be refined that quantify the intensity reduction due to the mean square displacements of atoms about their average positions. It is becoming increasingly apparent that ADPs constitute equally important structural information as atom positions and site occupancies. Unusual, yet accurately determined, ADPs can provide telltale clues to interesting physical phenomena, e.g., approach of phase transitions, glass-like thermal conductivity, pathways for high ionic conductivity, and a variety positional disorders. Consequently, the demand for high quality ADPs is increasing, owing in part to our desire to understand and tune physical properties of technological materials. Temperature dependent neutron diffraction using single-crystals is perhaps the best possible method to determine precise individual ADPs, yet the number of these studies is surprisingly limited owing to the paucity of neutron sources and dedicated single-crystal neutron diffractometers. ADPs exhibit various temperature dependent behaviors, and can range from harmonic to anharmonic. Examples from work completed and ongoing at Oak Ridge National Laboratory (stephanite, triphylite, amblygonite, petalite, brucite, filled-skutterudites, gas clathrate hydrates, etc.) as well as previously published work will be reviewed with the aim to generalize insights and recommendations. Research conducted at ORNL's High Flux Isotope Reactor and Spallation Neutron Source was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy.

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Multilayer Diffraction Reveals That Colloidal Superlattices Approach the Structural Perfection of Single Crystals

10.26434/chemrxiv.13103507.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Stefano Toso ◽

Dmitry Baranov ◽

Davide Altamura ◽

Francesco Scattarella ◽

Jakob Dahl ◽

...

Keyword(s):

Structural Information ◽

Accurate Determination ◽

Diffraction Method ◽

Atomic Displacement ◽

Interparticle Spacing ◽

X Rays ◽

Structural Perfection ◽

Fitting Algorithm ◽

Atomic Displacement Parameters

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EXTREMELY LOW FREQUENCY (50Hz) MAGNETIC FIELD INFLUENCES PHYSICO-CHEMICAL PROPERTIES OF WATER

Environmental Engineering and Management Journal ◽

10.30638/eemj.2019.189 ◽

2019 ◽

Vol 18 (9) ◽

pp. 1987-1994

Author(s):

Mihaela Racuciu ◽

Horea Olosutean

Keyword(s):

Magnetic Field ◽

Low Frequency ◽

Chemical Properties ◽

Extremely Low Frequency ◽

Physico Chemical

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Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

Minerals ◽

10.3390/min11030272 ◽

2021 ◽

Vol 11 (3) ◽

pp. 272

Author(s):

Seungyeol Lee ◽

Huifang Xu ◽

Hongwu Xu ◽

Joerg Neuefeind

Keyword(s):

Crystal Structure ◽

Distribution Function ◽

Single Crystal ◽

Pair Distribution Function ◽

Atomic Displacement ◽

Single Crystal Xrd ◽

X Ray Diffraction ◽

X Ray ◽

Neutron Pair ◽

Atomic Displacement Parameters

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

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