scholarly journals Structure elements can be predicted using the contact volume among protein residues

2021 ◽  
Vol 18 (0) ◽  
pp. 50-59
Author(s):  
Yasumichi Takase ◽  
Yoichi Yamazaki ◽  
Yugo Hayashi ◽  
Sachiko Toma-Fukai ◽  
Hironari Kamikubo
Keyword(s):  
Protein Residues

scholarly journals Computational Modeling to Explain Why 5,5-Diarylpentadienamides are TRPV1 Antagonists

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1765
Author(s):  
Julio Caballero
Keyword(s):  
Transient Receptor Potential ◽  
Structural Information ◽  
Chemical Activation ◽  
Receptor Potential ◽  
Quantitative Structure Activity Relationship ◽  
Structural Features ◽  
Transient Receptor Potential Vanilloid ◽  
Protein Residues ◽  
Topological Features ◽  
Transient Receptor

Several years ago, the crystallographic structures of the transient receptor potential vanilloid 1 (TRPV1) in the presence of agonists and antagonists were reported, providing structural information about its chemical activation and inactivation. TRPV1’s activation increases the transport of calcium and sodium ions, leading to the excitation of sensory neurons and the perception of pain. On the other hand, its antagonistic inactivation has been explored to design analgesic drugs. The interactions between the antagonists 5,5-diarylpentadienamides (DPDAs) and TRPV1 were studied here to explain why they inactivate TRPV1. The present work identified the structural features of TRPV1–DPDA complexes, starting with a consideration of the orientations of the ligands inside the TRPV1 binding site by using molecular docking. After this, a chemometrics analysis was performed (i) to compare the orientations of the antagonists (by using LigRMSD), (ii) to describe the recurrent interactions between the protein residues and ligand groups in the complexes (by using interaction fingerprints), and (iii) to describe the relationship between topological features of the ligands and their differential antagonistic activities (by using a quantitative structure–activity relationship (QSAR) with 2D autocorrelation descriptors). The interactions between the DPDA groups and the residues Y511, S512, T550, R557, and E570 (with a recognized role in the binding of classic ligands), and the occupancy of isoquinoline or 3-hydroxy-3,4-dihydroquinolin-2(1H)-one groups of the DPDAs in the vanilloid pocket of TRPV1 were clearly described. Based on the results, the structural features that explain why DPDAs inactivate TRPV1 were clearly exposed. These features can be considered for the design of novel TRPV1 antagonists.

scholarly journals Oxidative Modification of Native Protein Residues Using Cerium(IV) Ammonium Nitrate

2011 ◽  
Vol 133 (42) ◽  
pp. 16970-16976 ◽  
Author(s):  
Kristen L. Seim ◽  
Allie C. Obermeyer ◽  
Matthew B. Francis
Keyword(s):  
Ammonium Nitrate ◽  
Oxidative Modification ◽  
Native Protein ◽  
Protein Residues ◽  
Cerium Iv Ammonium Nitrate

scholarly journals Alphavirus Virulence Determinants

Pathogens ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 981
Author(s):  
Margarita V. Rangel ◽  
Kenneth A. Stapleford
Keyword(s):  
Viral Infections ◽  
Specific Protein ◽  
Chronic Arthritis ◽  
Virulence Determinants ◽  
Genetic Determinants ◽  
Protein Residues ◽  
Molecular Determinants ◽  
Public Health Threat ◽  
Significant Public Health ◽  
New Strategies

Alphaviruses are important pathogens that continue to cause outbreaks of disease in humans and animals worldwide. Diseases caused by alphavirus infections include acute symptoms of fever, rash, and nausea as well as chronic arthritis and severe-to-fatal conditions including myocarditis and encephalitis. Despite their prevalence and the significant public health threat they pose, there are currently no effective antiviral treatments or vaccines against alphaviruses. Various genetic determinants of alphavirus virulence, including genomic RNA elements and specific protein residues and domains, have been described by researchers to play key roles in the development of disease, the immune response to infection, and virus transmissibility. Here, we focus on the determinants that are currently described in the literature. Understanding how these molecular determinants shape viral infections can lead to new strategies for the development of therapies and vaccines to combat these viruses.

scholarly journals Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings

2018 ◽  
Vol 19 (11) ◽  
pp. 3315 ◽  
Author(s):  
Rita Pancsa ◽  
Fruzsina Zsolyomi ◽  
Peter Tompa
Keyword(s):  
Large Scale ◽  
Intrinsically Disordered Proteins ◽  
Protein Structures ◽  
Disordered Proteins ◽  
Cellular Interaction ◽  
Structural Constraints ◽  
Protein Residues ◽  
Intrinsically Disordered ◽  
Evolutionary Changes ◽  
Folded Proteins

Although improved strategies for the detection and analysis of evolutionary couplings (ECs) between protein residues already enable the prediction of protein structures and interactions, they are mostly restricted to conserved and well-folded proteins. Whereas intrinsically disordered proteins (IDPs) are central to cellular interaction networks, due to the lack of strict structural constraints, they undergo faster evolutionary changes than folded domains. This makes the reliable identification and alignment of IDP homologs difficult, which led to IDPs being omitted in most large-scale residue co-variation analyses. By preforming a dedicated analysis of phylogenetically widespread bacterial IDP–partner interactions, here we demonstrate that partner binding imposes constraints on IDP sequences that manifest in detectable interprotein ECs. These ECs were not detected for interactions mediated by short motifs, rather for those with larger IDP–partner interfaces. Most identified coupled residue pairs reside close (<10 Å) to each other on the interface, with a third of them forming multiple direct atomic contacts. EC-carrying interfaces of IDPs are enriched in negatively charged residues, and the EC residues of both IDPs and partners preferentially reside in helices. Our analysis brings hope that IDP–partner interactions difficult to study could soon be successfully dissected through residue co-variation analysis.

scholarly journals Solution Structure of Parathyroid Hormone Related Protein (Residues 1–34) Containing an Ala Substituted for an Ile in Position 15 (PTHrP[Ala15]-(1–34))

1997 ◽  
Vol 272 (47) ◽  
pp. 29572-29578 ◽  
Author(s):  
Julian A. Barden ◽  
Ruth M. Cuthbertson ◽  
Wu Jia-Zhen ◽  
Jane M. Moseley ◽  
Bruce E. Kemp
Keyword(s):  
Parathyroid Hormone ◽  
Solution Structure ◽  
Related Protein ◽  
Protein Residues ◽  
Parathyroid Hormone Related Protein

scholarly journals Bioinspired Thiophosphorodichloridate Reagents for Chemoselective Histidine Bioconjugation

2018 ◽  
Author(s):  
Shang Jia ◽  
Christopher Chang
Keyword(s):  
Protein Function ◽  
Living Cells ◽  
Covalent Modification ◽  
Native Protein ◽  
Selective Labeling ◽  
Protein Residues ◽  
Mild Conditions ◽  
Starting Point ◽  
Histidine Phosphorylation ◽  
Site Selective

Site-selective bioconjugation to native protein residues is a powerful tool for protein functionalization, with cysteine and lysine side chains being the most common points for attachment owing to their high nucleophilicity. We now report a strategy for histidine modification using thiophosphorodichloridate reagents that mimic post-translational histidine phosphorylation, enabling fast and selective labeling of protein histidines under mild conditions where various payloads can be introduced via copper-assisted alkyne-azide cycloaddition (CuAAC) chemistry. We establish that these reagents are particularly effective at covalent modification of His-tags, which are common motifs to facilitate protein purification, as illustrated by selective attachment of polyarginine cargoes to enhance the uptake of proteins into living cells. This work provides a starting point for probing and enhancing protein function using histidine-directed chemistry.

Abstract 3490: Mechanistic Involvement of Myeloperoxidase in the Pathogenesis of Atrial Fibrillation

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Volker Rudolph ◽  
Rene Andrie ◽  
Kai Friedrichs ◽  
Tanja K Rudolph ◽  
Anna Klinke ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Ex Vivo ◽  
Strong Association ◽  
Neutrophil Activation ◽  
Right Atrial ◽  
Atrial Myocytes ◽  
Knock Out ◽  
Protein Residues ◽  
Heme Enzyme ◽  
Knock Out Mice

Background: Observational clinical and ex-vivo studies have established a strong association between atrial fibrillation (AF) and inflammation. However, whether inflammation is cause or consequence of AF and which specific inflammatory mediators increase atrial susceptibility to fibrillate remain elusive. Herein, we provide evidence for mechanistic involvement of myeloperoxidase (MPO), a heme enzyme abundantly expressed by neutrophils, in the pathophysiology of AF. Methods and Results: Patients with AF assessed by pacemaker interrogation not only exhibited higher circulating plasma levels of MPO (503.1 [IR:404.6 –880.7] vs. 437.8 [IR:348.9 – 488.0 pmol/l; p=0.03; n=42), they also revealed an increased MPO burden in explanted left atrial tissue as compared to patients devoid of AF. In AF-patients MPO co-localized with markedly increased formation of 3-nitro and 3-chlorotyrosin, protein oxidations known to be catalyzed by MPO. Myeloperoxidase knock-out mice, pretreated with angiotensin II infusion for 2 weeks yielding increased neutrophil activation, revealed strikingly attenuated vulnerability for AF during right atrial electrophysiological stimulation as compared to wild type mice (probability of AF-induction: 3.0 vs. 12.7%; p<0.01). Whereas the electrical homogeneity of the atrial myocytes was not altered between the groups, atria of MPO knock out mice were indicative of significantly reduced atrial fibrosis and markedly reduced formation of 3-chloro- and 3-nitrotyrosine. Conclusion: In conclusion, the current findings not only underscore the significance of neutrophil activation as a critical pathophysiological prerequisite of AF, but reveal that MPO - by oxidatively modifying protein residues and increasing fibrosis of atrial myocytes - is causally linked to the initiation and perpetuation of AF.

Synthesis, spectroscopic (FT–IR and UV–Vis), crystallographic and theoretical studies, and a molecular docking simulation of an imatinib-like template

2019 ◽  
Vol 75 (12) ◽  
pp. 1681-1689
Author(s):  
Rodolfo Moreno-Fuquen ◽  
Kevin Arango-Daraviña ◽  
Esteban Garcia ◽  
Juan-C. Tenorio ◽  
Javier Ellena
Keyword(s):  
Crystal Growth ◽  
Hydrogen Bonds ◽  
Docking Simulation ◽  
Myelogenous Leukemia ◽  
Amino Group ◽  
Protein Residues ◽  
Function Analyzer ◽  
Stretching Vibration ◽  
Donor Acceptor ◽  
Ft Ir

The aim of the present study was to report the crystal structure and spectroscopic, electronic, supramolecular and electrostatic properties of a new polymorph of 4-(pyridin-2-yl)pyrimidin-2-amine (C9H8N4). The compound was synthesized under microwave irradiation. The single-crystal X-ray structure analysis revealed an angle of 13.36 (8)° between the planes of the rings, as well as molecules linked by Nsp 2—H...N hydrogen bonds forming dimers along the crystal. The material was analyzed by FT–IR vibrational spectroscopy, while a computational approach was used to elucidate the vibrational frequency couplings. The existence of Nsp 2—H...N hydrogen bonds in the crystal was confirmed spectroscopically by the IR peaks from the N—H stretching vibration shifting to lower wavenumbers in the solid state relative to those in the gas phase. The supramolecular studies confirmed the formation of centrosymmetric R 2 2(8) rings, which correspond to the formation of dimers that stack parallel to the b direction. Other weak C—H...π interactions, essential for crystal growth, were found. The UV–Vis spectroscopic analysis showed a donor–acceptor process, where the amino group acts as a donor and the pyridine and pyrimidine rings act as acceptors. The reactive sites of the molecule were identified and their quantitative values were defined using the electrostatic potential model proposed in the multifunctional wave function analyzer multiwfn. The calculated interaction energies between pairs of molecules were used to visualize the electrostatic terms as the leading factors against the dispersion factors in the crystal-growth process. The docking results showed that the amino group of the pyrimidine moiety was simultaneously anchored by hydrogen-bonding interactions with the Asp427 and His407 protein residues. This compound could be key for the realization of a series of syntheses of molecules that could be used as possible inhibitors of chronic myelogenous leukemia.

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