scholarly journals Exploring ligand dynamics in protein crystal structures with ensemble refinement

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.

Incommensurate modulation of calcium barium niobate (CBN28 and Ce:CBN28)

2012 ◽  
Vol 68 (2) ◽  
pp. 101-106 ◽  
Author(s):  
Heribert A. Graetsch ◽  
Chandra Shekhar Pandey ◽  
Jürgen Schreuer ◽  
Manfred Burianek ◽  
Manfred Mühlberg
Keyword(s):  
Crystal Structures ◽  
Tungsten Bronze ◽  
Atomic Displacement ◽  
Type Structure ◽  
Formula Unit ◽  
Tetragonal Tungsten Bronze ◽  
First Order ◽  
Oxygen Coordination ◽  
Incommensurate Modulation ◽  
Atomic Displacement Parameters

The incommensurately modulated crystal structures of Ca0.28Ba0.72Nb2O6 (CBN28) and Ce0.02Ca0.25Ba0.72Nb2O6 (Ce:CBN28) were refined in the supercentred setting X4bm(AA0,−AA0) of the 3 + 2-dimensional superspace group P4bm(aa½,−aa½). Both compounds are isostructural with a tetragonal tungsten bronze-type structure. The modulation of CBN28 consists of a wavy distribution of Ba and Ca atoms as well as vacancies on the incompletely occupied Me2 site with 15-fold oxygen coordination. The occupational modulation is coupled with a modulation of the atomic displacement parameters and a very weak modulation of the positional parameters of Me2. The surrounding O atoms show strong displacive modulations with amplitudes up to ca 0.2 Å owing to the cooperative tilting of the rigid NbO6 octahedra. The Me1 site with 12-fold coordination and Nb atoms are hardly affected by the modulations. Only first-order satellites were observed and the modulations are described by first-order harmonics. In Ce:CBN28 cerium appears to be located on both the Me2 and Me1 sites. Wavevectors and structural modulations are only weakly modified upon substitutional incorporation of 0.02 cerium per formula unit of calcium.

scholarly journals 4094 Structural Determinants of Immunogenicity for Peptide-Based Immunotherapy

2020 ◽  
Vol 4 (s1) ◽  
pp. 16-16
Author(s):  
Jason Devlin ◽  
Jesus Alonso ◽  
Grant Keller ◽  
Sara Bobisse ◽  
Alexandre Harari ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
T Cell ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
T Cell Receptor ◽  
Tumor Regression ◽  
Recombinant Expression ◽  
Cell Receptor ◽  
Protein Crystal ◽  
Dynamics Simulations

OBJECTIVES/GOALS: Neoantigen vaccine immunotherapies have shown promise in clinical trials, but identifying which peptides to include in a vaccine remains a challenge. We aim to establish that molecular structural features can help predict which neoantigens to target to achieve tumor regression. METHODS/STUDY POPULATION: Proteins were prepared by recombinant expression in E. coli followed by in vitro refolding. Correctly folded proteins were purified by chromatography. Affinities of protein-protein interactions were measured by surface plasmon resonance (SPR) and thermal stabilities of proteins were determined by differential scanning fluorimetry. All experiments were performed at least in triplicate. Protein crystals were obtained by hanging drop vapor diffusion. The protein crystal structures were solved by molecular replacement and underwent several rounds of automated refinement. Molecular dynamics simulations were performed using the AMBER molecular dynamics package. RESULTS/ANTICIPATED RESULTS: A T cell receptor (TCR) expressed by tumor-infiltrating T cells exhibited a 20-fold stronger binding affinity to the neoantigen peptide compared to the self-peptide. X-ray crystal structures of the peptides with the major histocompatibility complex (MHC) protein demonstrated that a non-mutated residue in the peptide samples different positions with the mutation. The difference in conformations of the non-mutated residue was supported by molecular dynamics simulations. Crystal structures of the TCR engaging both peptide/MHCs suggested that the conformation favored by the mutant peptide was crucial for TCR binding. The TCR bound the neoantigen/MHC with faster binding kinetics. DISCUSSION/SIGNIFICANCE OF IMPACT: Our results suggest that the mutation impacts the conformation of another residue in the peptide, and this alteration allows for more favorable T cell receptor binding to the neoantigen. This highlights the potential of non-mutated residues in contributing to neoantigen recognition.

scholarly journals Local and global analysis of macromolecular atomic displacement parameters

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.

Energetic materials: variable-temperature crystal structures of two biguanidinium dinitramides

2003 ◽  
Vol 36 (6) ◽  
pp. 1334-1341 ◽  
Author(s):  
Nadezhda B. Bolotina ◽  
Michaele J. Hardie ◽  
A. Alan Pinkerton
Keyword(s):  
Thermal Expansion ◽  
Crystal Structures ◽  
Energetic Materials ◽  
Variable Temperature ◽  
Atomic Displacement ◽  
Thermal Motion ◽  
Linear Temperature Dependence ◽  
Linear Temperature ◽  
Thermal Displacements ◽  
Atomic Displacement Parameters

The crystal structures of the energetic materials biguanidinium mono-dinitramide C2H8N{}_{5}^{\,+}.N3O{}_{4}^{\,-}, (BIGH)(DN), and biguanidinium bis-dinitramide C2H9N{}_{5}^{\,2+}.2N3O{}_{4}^{\,-}, (BIGH2)(DN)2, have been determined at several temperatures in the range 85–298 K using single-crystal X-ray diffraction techniques. The thermal expansion second-rank tensors have been determined to describe the thermal behavior of the crystals studied. Strongly anisotropic thermal expansion is most important in the direction perpendicular to the least-squares planes of the dinitramide ions in both cases, suggesting that the atomic thermal motion is significantly anharmonic in these crystals. Anharmonicity of thermal motion is also evident from the non-linear temperature dependence of the atomic displacement parameters. Rigid-body analysis of thermal motion both of dinitramide anions and of biguanidinium cations was performed using the libration and translation second-rank tensors. For both compounds, the libration thermal motion is strongly anisotropic with the dominating libration axes oriented in a similar manner in both anions and cations. Although the translation motion of the ions is not strongly anisotropic, the axes of largest thermal displacements are close to the directions of greatest thermal expansion of the crystals.

scholarly journals Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

2015 ◽  
Vol 71 (11) ◽  
pp. 2192-2202 ◽  
Author(s):  
Lada Biedermannová ◽  
Bohdan Schneider
Keyword(s):  
Amino Acid ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Solvent Accessibility ◽  
Hydration Shell ◽  
Protein Crystal ◽  
Water Molecules ◽  
Amino Acid Residues ◽  
Set Up ◽  
Dynamics Simulations

Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

scholarly journals Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin

2012 ◽  
Vol 68 (2) ◽  
pp. 119-123 ◽  
Author(s):  
Julian C.-H. Chen ◽  
Zoë Fisher ◽  
Andrey Y. Kovalevsky ◽  
Marat Mustyakimov ◽  
B. Leif Hanson ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Room Temperature ◽  
Protein Structures ◽  
Atomic Displacement ◽  
Protein Crystal ◽  
X Ray Diffraction ◽  
Resolution Time ◽  
X Ray ◽  
Two Temperatures ◽  
Atomic Displacement Parameters

The room-temperature (RT) X-ray structure of H/D-exchanged crambin is reported at 0.85 Å resolution. As one of the very few proteins refined with anisotropic atomic displacement parameters at two temperatures, the dynamics of atoms in the RT and 100 K structures are compared. Neutron diffraction data from an H/D-exchanged crambin crystal collected at the Protein Crystallography Station (PCS) showed diffraction beyond 1.1 Å resolution. This is the highest resolution neutron diffraction reported to date for a protein crystal and will reveal important details of the anisotropic motions of H and D atoms in protein structures.

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

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Viktor Ahlberg Gagnér ◽  
Ida Lundholm ◽  
Maria-Jose Garcia-Bonete ◽  
Helena Rodilla ◽  
Ran Friedman ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Structural Information ◽  
Low Frequency ◽  
Chemical Properties ◽  
Atomic Displacement ◽  
Thz Radiation ◽  
X Ray Crystallography ◽  
Bovine Trypsin ◽  
Main Challenge ◽  
Atomic Displacement Parameters

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.

scholarly journals Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures

RSC Advances ◽  
2020 ◽  
Vol 10 (14) ◽  
pp. 8435-8443
Author(s):  
Octav Caldararu ◽  
Majda Misini Ignjatović ◽  
Esko Oksanen ◽  
Ulf Ryde
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Water Structure ◽  
Protein Crystal ◽  
Local Clustering ◽  
Dynamics Simulations ◽  
Structure In Solution

Molecular dynamics simulations can reproduce the water structure around proteins in crystal structure only if a local clustering is performed.

Reliability of atomic displacement parameters in protein crystal structures

1999 ◽  
Vol 55 (2) ◽  
pp. 473-478 ◽  
Author(s):  
Oliviero Carugo ◽  
Patrick Argos
Keyword(s):  
Protein Structures ◽  
Atomic Displacement ◽  
Protein Crystal ◽  
Nonlinear Dependence ◽  
Standard Errors ◽  
Unexpected Result ◽  
Protein Chain ◽  
Space Groups ◽  
Structure Determinations ◽  
Atomic Displacement Parameters

Mean standard errors in atomic displacement parameters (ADPs) resulting from protein crystal structure determinations are estimated by comparing the ADPs of protein-chain pairs of identical sequence within the same crystal or within different crystals displaying the same or different space groups. The estimated ADP standard errors increase nearly linearly as the resolution decreases – an unexpected result given the nonlinear dependence of the resolution on the amount of diffraction data. The estimated ADP standard errors are larger for side-chain and solvent-exposed atoms than for main-chain and buried atoms and, surprisingly, are also larger for residues in the helical secondary structure relative to other local backbone conformations. The results allow an estimate of the influence of crystallographic refinement restraints on ADP standard errors. Such corrections should be applied when comparing different protein structures.

scholarly journals Temperature-resolved study of three [M(M′O4)4(TBPO)4] complexes (MM′ = URe, ThRe, ThTc)

2006 ◽  
Vol 62 (1) ◽  
pp. 68-85 ◽  
Author(s):  
Madeleine Helliwell ◽  
David Collison ◽  
Gordon H. John ◽  
Iain May ◽  
Mark J. Sarsfield ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Room Temperature ◽  
Atomic Displacement ◽  
The Body ◽  
Group Symmetry ◽  
Orthorhombic Space Group ◽  
Space Group Symmetry ◽  
Space Group ◽  
Group I ◽  
Atomic Displacement Parameters

The crystal structures of the title complexes were measured at several temperatures between room temperature and 100 K. Each sample shows reversible crystal-to-crystal phase transitions as the temperature is varied. The behaviour of [U(ReO4)4(TBPO)4] (I) and [Th(ReO4)4(TBPO)4] (II) (TBPO = tri-n-butylphosphine oxide) is very similar; at room temperature, crystals of (I) and (II) are isostructural, with space group I\bar 42m, and reducing the temperature to 100 K causes a lowering of the space-group symmetry to C-centred cells, space groups Cc for (I) and Cmc21 for (II). The variation of lattice symmetry of [Th(TcO4)4(TBPO)4] (III) was found to be somewhat different, with the body-centred cubic space group, I\bar 43m, occurring at 293 K, a reduction of symmetry at 230 K to the C-centred orthorhombic space group, Cmc21, and a further transition to the primitive orthorhombic space group, Pbc21, below 215 K. Elucidation of the correct space-group symmetry and the subsequent refinement was complicated in some cases by the twinning by pseudo-merohedry that arises from the lowering of the space-group symmetry, occurring as the temperature is reduced. All three of the crystal structures determined at room temperature have high atomic displacement parameters, particularly of the n Bu groups, and (III) shows disorder of some of the O atoms. The structures in the space group Cmc21, show some disorder of n Bu groups, but are otherwise reasonably well ordered; the structures of (I) in Cc and (III) in Pbc21 are ordered, even to the ends of the alkyl chains. Inter-comparison of the structures measured below 293 K, using the program OFIT from the SHELXTL package, showed that generally, they are remarkably alike, with weighted r.m.s. deviations of the M, M′ and P atoms of less than 0.1 Å, as are the 293 K structures of (I) and (II) with their low-temperature counterparts. However, the structure of (III) measured in the space group Cmc21 is significantly different from both the structure of (III) at 293 K and that found below 215 K, with weighted r.m.s. deviations of the Th, Tc and P atoms of 0.40 and 0.37 Å, respectively. An extensive network of weak intra- and intermolecular C—H...O hydrogen bonds found between the atoms of the n Bu and [M′O4] groups probably influences the packing and the overall geometry of the molecules.

Sign in / Sign up

Export Citation Format

Share Document