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https://www.readbyqxmd.com/read/28097693/distinguishing-between-biochemical-and-cellular-function-are-there-peptide-signatures-for-cellular-function-of-proteins
#1
Shruti Jain, Kausik Bhattacharyya, Rachit Bakshi, Ankita Narang, Vani Brahmachari
The genome annotation and identification of gene function depends on conserved biochemical activity. However, in the cell, proteins with the same biochemical function can participate in different cellular pathways and cannot complement one another. Similarly, two proteins of very different biochemical functions are put in the same class of cellular function; for example, the classification of a gene as an oncogene or a tumour suppressor gene is not related to its biochemical function, but is related to its cellular function...
January 18, 2017: Proteins
https://www.readbyqxmd.com/read/28097692/structural-role-of-a-conserved-active-site-cis-proline-in-the-thermotoga-maritima-acetyl-esterase-from-the-carbohydrate-esterase-family-7
#2
Mrityunjay K Singh, Narayanan Manoj
A conserved cis proline residue located in the active site of Thermotoga maritima acetyl esterase (TmAcE) from the carbohydrate esterase family 7 (CE7) has been substituted by alanine. The residue was known to play a crucial role in determining the catalytic properties of the enzyme. To elucidate the structural role of the residue, the crystal structure of the Pro228Ala variant (TmAcEP228A ) was determined at 2.1 Å resolution. The replacement does not affect the overall secondary, tertiary and quaternary structures and moderately decreases the thermal stability...
January 18, 2017: Proteins
https://www.readbyqxmd.com/read/28097686/context-characterization-of-amino-acid-homorepeats-using-evolution-position-and-order
#3
Pablo Mier, Gregorio Alanis-Lobato, Miguel A Andrade-Navarro
Amino acid repeats, or homorepeats, are low complexity protein motifs consisting of tandem repetitions of a single amino acid. Their presence and relative number vary in different proteomes, and some studies have tried to address this variation, proteome by proteome. In this work, we present a full characterization of amino acid homorepeats across evolution. We studied the presence and differential usage of each possible homorepeat in proteomes from various taxonomic groups, using clusters of very similar proteins to eliminate redundancy...
January 18, 2017: Proteins
https://www.readbyqxmd.com/read/28076882/characterization-of-salmonella-typhi-ompc-and-ompf-porins-engineered-with-hiv-gp41-epitope-on-the-surface-loops
#4
Madhuranayaki Thulasingam, Subha Damodharan, Gopal Madhana Vigneshwari, Eswari P J Pandaranayaka, Luke Elizabeth Hanna, Ramakrishnan Usha, Sankaran Krishnaswamy
Porins form trimers in the outer membrane and help transport nutrients and waste products across the bacterial cell membrane. Porin loops are suitable candidates as display systems due to their high immunogenicity and presentation at the bacterial cell surface. In this study, Salmonella typhi porins (OmpC and OmpF) engineered with the Kennedy peptide from gp41 of HIV were characterised. The chimeric OmpC carrying the Kennedy peptide in loop7 did not trimerise, whereas the chimeric OmpF with the epitope in loop5 formed trimers and also was recognised by the antibodies in the HIV patient serum...
January 11, 2017: Proteins
https://www.readbyqxmd.com/read/28066924/side-chain-flexibility-and-coupling-between-the-s4-s5-linker-and-the-trp-domain-in-thermo-sensitive-trp-channels-insights-from-protein-modeling
#5
Sergio Romero-Romero, Froylan Gómez-Lagunas, Daniel Balleza
The transient receptor potential (TRP) superfamily is subdivided into several subfamilies on the basis of sequence similarity, which is highly heterogeneous but shows a molecular architecture that resembles the one present in members of the Kv channel superfamily. Because of this diversity, they produce a large variety of channels with different gating and permeability properties. Elucidation of these particular features necessarily requires comparative studies based on structural and functional data. The present study aims to compilate, analyze, and determine, in a coherent way, the relationship between intrinsic side-chain flexibility and the allosteric coupling in members of the TRPV, TRPM, and TRPC families...
January 9, 2017: Proteins
https://www.readbyqxmd.com/read/28066922/x-ray-crystal-structure-of-the-n-terminal-region-of-moloney-murine-leukemia-virus-integrase-and-its-implications-for-viral-dna-recognition
#6
Rongjin Guan, Sriram Aiyer, Marie L Cote, Rong Xiao, Mei Jiang, Thomas B Acton, Monica J Roth, Gaetano T Montelione
The retroviral integrase (IN) carries out the integration of a dsDNA copy of the viral genome into the host DNA, an essential step for viral replication. All IN proteins have three general domains, the N-terminal domain (NTD), the catalytic core domain (CCD), and the C-terminal domain (CTD). The NTD includes an HHCC zinc finger-like motif, which is conserved in all retroviral IN proteins. Two crystal structures of Moloney murine leukemia virus (M-MuLV) IN N-terminal region (NTR) constructs that both include an N-terminal extension domain (NED, residues 1-44) and an HHCC zinc-finger NTD (residues 45-105), in two crystal forms are reported...
January 9, 2017: Proteins
https://www.readbyqxmd.com/read/28066917/balancing-exploration-and-exploitation-in-population-based-sampling-improves-fragment-based-de-novo-protein-structure-prediction
#7
David Simoncini, Thomas Schiex, Kam Y J Zhang
Conformational search space exploration remains a major bottleneck for protein structure prediction methods. Population-based meta-heuristics typically enable the possibility to control the search dynamics and to tune the balance between local energy minimization and search space exploration. EdaFold is a fragment-based approach that can guide search by periodically updating the probability distribution over the fragment libraries used during model assembly. We implement the EdaFold algorithm as a Rosetta protocol and provide two different probability update policies: a cluster-based variation (EdaRosec ) and an energy-based one (EdaRoseen ) We analyze the search dynamics of our new Rosetta protocols and show that EdaRosec EdaRosec is able to provide predictions with lower Cα RMSD to the native structure than EdaRoseen and Rosetta AbInitio Relax protocol...
January 9, 2017: Proteins
https://www.readbyqxmd.com/read/28066915/crystallographic-analysis-of-murine-p24%C3%AE-2-golgi-dynamics-gold-domain
#8
Masamichi Nagae, Dorothee Liebschner, Yusuke Yamada, Kana Morita-Matsumoto, Naohiro Matsugaki, Toshiya Senda, Morihisa Fujita, Taroh Kinoshita, Yoshiki Yamaguchi
The p24 family proteins form homo- and hetero-oligomeric complexes for efficient transport of cargo proteins from the endoplasmic reticulum to the Golgi apparatus. It consists of four subfamilies (p24α, p24β, p24γ and p24δ). p24γ2 plays crucial roles in the selective transport of glycosylphosphatidylinositol-anchored proteins. Here we determined the crystal structure of mouse p24γ2 Golgi dynamics (GOLD) domain at 2.8 Å resolution by the single anomalous diffraction method using intrinsic sulfur atoms...
January 9, 2017: Proteins
https://www.readbyqxmd.com/read/28056499/recognition-of-hiv-inactivating-peptide-triazoles-by-the-recombinant-soluble-env-trimer-bg505-sosip-664
#9
Kriti Acharya, Adel A Rashad, Francesca Moraca, Per Johan Klasse, John P Moore, Cameron Abrams, Irwin Chaiken
Peptide triazole (PT) antagonists interact with gp120 subunits of HIV-1 Env trimers to block host cell receptor interactions, trigger gp120 shedding, irreversibly inactivate virus and inhibit infection. Despite these enticing functions, understanding the structural mechanism of PT-Env trimer encounter has been limited. In this work, we combined competition interaction analysis and computational simulation to demonstrate PT binding to the recombinant soluble trimer, BG505 SOSIP.664, a stable variant that resembles native virus spikes in binding to CD4 receptor as well as known conformationally-dependent Env antibodies...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28056497/taxonomic-distribution-repeats-and-functions-of-the-s1-domain-containing-proteins-as-members-of-the-ob-fold-family
#10
Evgeniia I Deryusheva, Andrey V Machulin, Olga M Selivanova, Oxana V Galzitskaya
Proteins of the nucleic acid-binding proteins superfamily perform such functions as of processing, transport, storage, stretching, translation and degradation of RNA. It is one of the 16 superfamilies containing the OB-fold in protein structures. Here, we have analyzed the superfamily of nucleic acid-binding proteins (the number of sequences exceeds 200000) and obtained that this superfamily prevalently consists of proteins containing the cold shock DNA-binding domain (about 131000 protein sequences). Proteins containing the S1 domain compose 57% from the cold shock DNA-binding domain family...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28056492/insights-into-the-interaction-of-high-potency-inhibitor-irc-083864-with-phosphatase-cdc25
#11
Manal Sarkis, Maria A Miteva, Maria Chiara Dasso Lang, Maryse Jaouen, Marie-Agnès Sari, Marie-Odile Galcéra, Mélanie Ethève-Quelquejeu, Christiane Garbay, Gildas Bertho, Emmanuelle Braud
CDC25 phosphatases play a crucial role in cell cycle regulation. They have been found to be over-expressed in various human tumours and to be valuable targets for cancer treatment. Here, we report the first model of binding of the most potent CDC25 inhibitor to date, the bis-quinone IRC-083864, into CDC25B obtained by combining molecular modeling and NMR studies. Our study provides new insights into key interactions of the catalytic site inhibitor and CDC25B in the absence of any available experimental structure of CDC25 with a bound catalytic site inhibitor...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28056488/molecular-dynamics-simulations-reveal-structural-insights-into-inhibitor-binding-modes-and-functionality-in-human-group-iia-phospholipase-a2
#12
Ryung Rae Kim, Alpeshkumar K Malde, Alireza Nematollahi, Kieran F Scott, W Bret Church
Human group IIA phospholipase A2 (hGIIA) promotes inflammation in immune-mediated pathologies by regulating the arachidonic acid pathway through both catalysis-dependent and -independent mechanisms. The hGIIA crystal structure, both alone and inhibitor-bound, together with structures of closely related snake-venom-derived secreted phospholipase enzymes has been well described. However, differentiation of biological and non-biological contacts and the relevance of structures determined from snake venom enzymes to human enzymes are not clear...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28056486/dynamics-of-bridge-helix-bending-in-rna-polymerase-ii
#13
Zhan-Feng Wang, Yi-Ben Fu, Peng-Ye Wang, Ping Xie
One of critical issues for RNA polymerase is how the enzyme translocates along the DNA substrate during transcription elongation cycle. Comparisons of the structure of RNA polymerase II (Pol II) with that of bacterial enzyme have suggested that the transition of the bridge helix (BH) from straight to flipped-out conformations facilitates the translocation of upstream DNA-RNA hybrid. However, the flipped-out conformation of BH in Pol II has not been observed up to now and the detailed mechanism of how the BH facilitating upstream hybrid translocation still remains obscure...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28026062/addressing-recent-docking-challenges-a-hybrid-strategy-to-integrate-template-based-and-free-protein-protein-docking
#14
Yumeng Yan, Zeyu Wen, Xinxiang Wang, Sheng-You Huang
Protein-protein docking is an important computational tool for predicting protein-protein interactions. With the rapid development of proteomics projects, more and more experimental binding information ranging from mutagenesis data to three-dimensional structures of protein complexes are becoming available. Therefore, how to appropriately incorporate the biological information into traditional ab initio docking has been an important issue and challenge in the field of protein-protein docking. To address these challenges, we have developed a Hybrid DOCKing protocol of template-based and template-free approaches, referred to as HDOCK...
December 27, 2016: Proteins
https://www.readbyqxmd.com/read/28019699/conformational-stability-of-the-epidermal-growth-factor-egf-receptor-as-influenced-by-glycosylation-dimerization-and-egf-hormone-binding
#15
Eric S Taylor, Laercio Pol-Fachin, Roberto D Lins, Steven K Lower
The epidermal growth factor receptor (EGFR) is an important transmembrane glycoprotein kinase involved the initiation or perpetuation of signal transduction cascades within cells. These processes occur after EGFR binds to a ligand [epidermal growth factor (EGF)], thus inducing its dimerization and tyrosine autophosphorylation. Previous publications have highlighted the importance of glycosylation and dimerization for promoting proper function of the receptor and conformation in membranes; however, the effects of these associations on the protein conformational stability have not yet been described...
December 26, 2016: Proteins
https://www.readbyqxmd.com/read/28019690/structural-analysis-of-oligomeric-and-protofibrillar-a%C3%AE-amyloid-pair-structures-considering-f20l-mutation-effects-using-molecular-dynamics-simulations
#16
Myeongsang Lee, Hyun Joon Chang, Inchul Baek, Sungsoo Na
Aβ amyloid proteins are involved in neuro-degenerative diseases such as Alzheimer's, Parkinson's, and so forth. Due to its structurally stable feature under physiological conditions, Aβ amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aβ amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aβ amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect...
December 26, 2016: Proteins
https://www.readbyqxmd.com/read/28019680/modeling-protein-assemblies-capri-15-years-hence-6-th-capri-evaluation-meeting-april-17-19-tel-aviv-israel
#17
EDITORIAL
Shoshana J Wodak, Joel Janin
No abstract text is available yet for this article.
December 26, 2016: Proteins
https://www.readbyqxmd.com/read/28002624/flexpepdock-lessons-from-capri-peptide-protein-rounds-and-suggested-new-criteria-for-assessment-of-model-quality-and-utility
#18
Orly Marcu, Emma-Joy Dodson, Nawsad Alam, Michal Sperber, Dima Kozakov, Marc F Lensink, Ora Schueler-Furman
CAPRI rounds 28 and 29 included, for the first time, peptide-receptor targets of three different systems, reflecting increased appreciation of the importance of peptide-protein interactions. The CAPRI rounds allowed us to objectively assess the performance of Rosetta FlexPepDock, one of the first protocols to explicitly include peptide flexibility in docking, accounting for peptide conformational changes upon binding. We discuss here successes and challenges in modeling these targets: we obtain top-performing, high-resolution models of the peptide motif for cases with known binding sites but there is a need for better modeling of flanking regions, as well as better selection criteria, in particular for unknown binding sites...
December 21, 2016: Proteins
https://www.readbyqxmd.com/read/28002620/the-effect-of-specific-proline-residues-on-the-kinetic-stability-of-the-triosephosphate-isomerases-of-two-trypanosomes
#19
Valeria Guzmán-Luna, Andrea G Quezada, A Jessica Díaz-Salazar, Nallely Cabrera, Ruy Pérez-Montfort, Miguel Costas
The effect of specific residues on the kinetic stability of two closely related triosephosphate isomerases (from Trypanosoma cruzi, TcTIM and Trypanosoma brucei, TbTIM) have been studied. Based on a comparison of their β-turn occurrence, we engineered two chimerical enzymes where their super secondary β-loop-α motifs 2 ((βα)2 ) were swapped. Differential scanning calorimetry (DSC) experiments showed that the (βα)2 motif of TcTIM inserted into TbTIM (2Tc) increases the kinetic stability. On the other hand, the presence of the (βα)2 motif of TbTIM inserted into TcTIM (2Tb) gave a chimerical protein difficult to purify in soluble form and with a significantly reduced kinetic stability...
December 21, 2016: Proteins
https://www.readbyqxmd.com/read/27936519/a-computational-approach-for-studying-antibody-antigen-interactions-without-prior-structural-information-the-anti-testosterone-binding-antibody-as-a-case-study
#20
Artturi Koivuniemi, Kristiina Takkinen, Tarja Nevanen
Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel the atomistic level properties of antibody-antigen complexes with the help of computational modeling. Thus, here we have studied the feasibility of computational tools to gather atomic scale information regarding the antibody-antigen complexes solely starting from an amino acid sequence. First, we constructed a homology model for the anti-testosterone binding antibody based on the knowledge based classification of complementary determining regions (CDRs) and implicit solvent molecular dynamics simulations...
December 9, 2016: Proteins
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