scholarly journals Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein–ligand complex structure analysis

2020 ◽  
Vol 11 (34) ◽  
pp. 9072-9087
Author(s):  
Masatoshi Maeki ◽  
Sho Ito ◽  
Reo Takeda ◽  
Go Ueno ◽  
Akihiko Ishida ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Room Temperature ◽  
Complex Structure ◽  
Protein Crystallography ◽  
Protein Crystal ◽  
Ligand Complex

Room temperature protein crystallography and its application to protein–ligand complex structure analysis was demonstrated using a microfluidic protein crystal array device.

scholarly journals Protein–ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation

2017 ◽  
Vol 73 (8) ◽  
pp. 702-709 ◽  
Author(s):  
Hisashi Naitow ◽  
Yoshinori Matsuura ◽  
Kensuke Tono ◽  
Yasumasa Joti ◽  
Takashi Kameshima ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Room Temperature ◽  
Complex Structure ◽  
Binding Mode ◽  
Ligand Complex ◽  
X Ray ◽  
Cell Parameters ◽  
Serial Femtosecond Crystallography ◽  
Small Molecule Ligand

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein–ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.

How many water molecules can be detected by protein crystallography?

1999 ◽  
Vol 55 (2) ◽  
pp. 479-483 ◽  
Author(s):  
Oliviero Carugo ◽  
Domenico Bordo
Keyword(s):  
Room Temperature ◽  
Protein Crystallography ◽  
Protein Crystal ◽  
Expected Improvement ◽  
Water Molecules ◽  
Asymmetric Unit ◽  
Protein Crystal Structure ◽  
Protein Models ◽  
Crystal Volume

The number of water molecules which are expected to be experimentally located by protein crystallography was determined by multiple regression analysis on a test set of 873 known protein crystal structures determined at room temperature and on another set of 33 structures determined at low temperature. The dependence of the number of water molecules included in the protein models as a function of a number of significant regressors, such as resolution, fraction of crystal volume occupied by the solvent, number of residues in the asymmetric unit, fraction of apolar protein surface or secondary structure, has been studied. The number of water molecules included in crystallographic models depends primarily on the resolution at which the structure has been solved, while the temperature of the data collection has only marginal influence. On average, at 2.0 Å resolution one water molecule per residue is included in the model, while at 1.0 Å resolution about 1.6–1.7 are crystallographically located. At 2.0 Å resolution the well known rule-of-thumb of `one water per protein residue' is confirmed, though the number of water molecules experimentally observed is strongly dependent on resolution. The results presented are useful in assessing the quality of a protein crystal structure, in selecting structural results to be compared and in evaluating the expected improvement on the solvent structure when increasing the crystallographic resolution.

scholarly journals An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation

2021 ◽  
Author(s):  
Nadendla EswarKumar ◽  
Cheng-Han Yang ◽  
Sunilkumar Tewary ◽  
Yi-Qi Yeh ◽  
Hsiao-Ching Yang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Complex ◽  
Tyrosine Phosphatase ◽  
Complex Structure ◽  
Protein Crystallography ◽  
Md Simulations ◽  
Integrative Approach ◽  
Single Mutation ◽  
Protein Protein Interactions ◽  
Transient Nature

AbstractProtein tyrosine phosphatase: phospho-protein complex structure determination, which requires to understand how specificity is achieved at the protein level remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we established an integrative workflow involving protein crystallography, SAXS and pTyr-tailored MD simulations to reveal the complex formed between rPTPεD1 and phospho-SrcKD, revealing transient protein–protein interactions distal to the active site. To support our finding, we determined the associate rate between rPTPεD1 and phospho-SrcKD and showed that a single mutation on rPTPεD1 disrupts this transient interaction, resulting in the reduction of association rate and activity. Our simulations suggest that rPTPεD1 employs a binding mechanism involving conformational change prior to the engagement of cSrcKD. This integrative approach is applicable to other PTP: phospho-protein complex determination and is a general approach for elucidating transient protein surface interactions.

scholarly journals Dissimilar Ligands Bind in a Similar Fashion: A Guide to Ligand Binding-Mode Prediction with Application to CELPP Studies

2021 ◽  
Vol 22 (22) ◽  
pp. 12320
Author(s):  
Xianjin Xu ◽  
Xiaoqin Zou
Keyword(s):  
Molecular Similarity ◽  
Complex Structure ◽  
Binding Mode ◽  
Molecular Structures ◽  
Complex Structures ◽  
Binding Modes ◽  
Ligand Complex ◽  
Systematic Analysis ◽  
Binding Mode Prediction ◽  
Similarity Principle

The molecular similarity principle has achieved great successes in the field of drug design/discovery. Existing studies have focused on similar ligands, while the behaviors of dissimilar ligands remain unknown. In this study, we developed an intercomparison strategy in order to compare the binding modes of ligands with different molecular structures. A systematic analysis of a newly constructed protein–ligand complex structure dataset showed that ligands with similar structures tended to share a similar binding mode, which is consistent with the Molecular Similarity Principle. More importantly, the results revealed that dissimilar ligands can also bind in a similar fashion. This finding may open another avenue for drug discovery. Furthermore, a template-guiding method was introduced for predicting protein–ligand complex structures. With the use of dissimilar ligands as templates, our method significantly outperformed the traditional molecular docking methods. The newly developed template-guiding method was further applied to recent CELPP studies.

scholarly journals Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+

2014 ◽  
Vol 70 (6) ◽  
pp. 814-818 ◽  
Author(s):  
Qun Wan ◽  
Andrey Y. Kovalevsky ◽  
Mark A. Wilson ◽  
Brad C. Bennett ◽  
Paul Langan ◽  
...  
Keyword(s):  
Dihydrofolate Reductase ◽  
Ternary Complex ◽  
Room Temperature ◽  
Catalytic Mechanism ◽  
National Laboratory ◽  
Complex Structure ◽  
Protonation State ◽  
Data Set ◽  
X Ray ◽  
Oak Ridge

A crystal ofEscherichia colidihydrofolate reductase (ecDHFR) complexed with folate and NADP+of 4 × 1.3 × 0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR–folate–NADP+ternary-complex structure in order to examine the protonation state, protein dynamics and solvent structure of the complex, furthering understanding of the catalytic mechanism.

scholarly journals Atran-analoge Verbindungen des Typs / Atrane Analogous Compounds of the Type

1984 ◽  
Vol 39 (3) ◽  
pp. 341-351 ◽  
Author(s):  
Joseph Grobe ◽  
Gerald Henkel ◽  
Bernt Krebs ◽  
Nikolaos Voulgarakis
Keyword(s):  
Structure Analysis ◽  
Nmr Spectra ◽  
Room Temperature ◽  
Trigonal Bipyramid ◽  
Angular Distortion ◽  
Type I ◽  
Tetrahedral Coordination ◽  
Cage Compounds ◽  
X Ray ◽  
H Nmr

Heterocyclic cage compounds of type I (compounds 8-10) have been prepared by condensation reactions of 1,2,2-trifunctional disilanes Me(R)XSiSiMeX2 (R = Me, Ph, OEt; X = NMe2, OEt) with triethanolamine using the “Dilution Principle”. The starting compounds are obtained by Si-Me cleavage of Si2Me6 with acetylchloride/AlCl3 followed by either aminolysis with HNMe2 or alcoholysis with EtOH. 1H NMR spectra indicate N→Si(1) intraction with the more acidic Si atom in 8 and 9. This result is proved by the X-ray structure analysis of 8 (monoclinic, P21/c; a = 7,088(2), b = 15,070(4), c = 12,701(4) Å, β = 104,96(2) at -130 °C, Z = 4); the Si(1)···N distance is found to be 2,768 Å , connected with a significant angular distortion of the tetrahedral coordination around Si(1) towards a trigonal bipyramid. In compound 10, too, N→Si(1) coordination is observed at room temperature in spite of almost equal acidity for both Si atoms. This can be explained by the preference of 5- over 6-membered chelating ring systems. At higher temperatures the 1H NMR spectra show a fluctuation of the N-donor between the two Si centres.

Facile Synthesis of 4,5-Dihydro-1,3,4-Thiadiazoles by 1,3-Dipolar Cycloaddition of Thioisomünchnones

2009 ◽  
Vol 62 (4) ◽  
pp. 356 ◽  
Author(s):  
Bárbara Sánchez ◽  
José Luis Bravo ◽  
María Josí Arívalo ◽  
Ignacio López ◽  
Mark E. Light ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Structure Elucidation ◽  
Room Temperature ◽  
Dipolar Cycloaddition ◽  
Two Dimensional ◽  
Facile Synthesis ◽  
X Ray ◽  
Mild Conditions ◽  
Nmr Techniques

The present paper summarizes a straightforward synthesis of 4,5-dihydro-1,3,4-thiadiazoles by the 1,3-dipolar cycloaddition of thioisomünchnones. These reactions have been carried out in dichloromethane and are essentially complete within 60 min at room temperature. Under such mild conditions the asymmetric version has been explored as well. Unequivocal structure elucidation has been accomplished by means of one- and two-dimensional NMR techniques as well as X-ray structure analysis.

scholarly journals Mass Spectrometric Analysis of Antibody—Epitope Peptide Complex Dissociation: Theoretical Concept and Practical Procedure of Binding Strength Characterization

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4776
Author(s):  
Bright D. Danquah ◽  
Kwabena F. M. Opuni ◽  
Claudia Roewer ◽  
Cornelia Koy ◽  
Michael O. Glocker
Keyword(s):  
Mass Spectrometry ◽  
Dissociation Constant ◽  
Gas Phase ◽  
Immune Complex ◽  
Room Temperature ◽  
Electrospray Mass Spectrometry ◽  
Small Sample ◽  
Epitope Peptide ◽  
Ligand Complex ◽  
Dissociation Constant Kd

Electrospray mass spectrometry is applied to determine apparent binding energies and quasi equilibrium dissociation constants of immune complex dissociation reactions in the gas phase. Myoglobin, a natural protein-ligand complex, has been used to develop the procedure which starts from determining mean charge states and normalized and averaged ion intensities. The apparent dissociation constant KD m0g#= 3.60 × 10−12 for the gas phase heme dissociation process was calculated from the mass spectrometry data and by subsequent extrapolation to room temperature to mimic collision conditions for neutral and resting myoglobin. Similarly, for RNAse S dissociation at room temperature a KD m0g#= 4.03 × 10−12 was determined. The protocol was tested with two immune complexes consisting of epitope peptides and monoclonal antibodies. For the epitope peptide dissociation reaction of the FLAG peptide from the antiFLAG antibody complex an apparent gas phase dissociation constant KD m0g#= 4.04 × 10−12 was calculated. Likewise, an apparent KD m0g#= 4.58 × 10−12 was calculated for the troponin I epitope peptide—antiTroponin I antibody immune complex dissociation. Electrospray mass spectrometry is a rapid method, which requires small sample amounts for either identification of protein-bound ligands or for determination of the apparent gas phase protein-ligand complex binding strengths.

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