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https://www.readbyqxmd.com/read/28205291/molecular-dynamics-simulation-study-of-the-stay-or-leave-problem-for-two-magnesium-ions-in-gene-transcription
#1
Shaogui Wu
Two magnesium ions play important roles in nucleotide addition cycle (NAC) of gene transcription. However, at the end of each NAC, why does one ion stay in the active site while the other ion leaves with product pyrophosphate (PPi )? This problem still remains obscure. In the present work, we studied the problem using all-atom molecular dynamics (MD) simulation combined with steered molecular dynamics (SMD) and umbrella sampling (US) simulation methods. Our simulations reveal that although both ions are located in the active site after chemistry, their detailed positions are not symmetrical, leading to their different forces from surrounding groups...
February 16, 2017: Proteins
https://www.readbyqxmd.com/read/28205250/crystal-structure-of-dibenzothiophene-sulfone-monooxygenase-bdsa-from-bacillus-subtilis-wu-s2b
#2
Masahiko Okai, Woo Cheol Lee, Li-Jun Guan, Takashi Ohshiro, Yoshikazu Izumi, Masaru Tanokura
The dibenzothiophene (DBT) sulfone monooxygenase BdsA from Bacillus subtilis WU-S2B catalyzes the conversion of DBT sulfone to 2'-hydroxybiphenyl 2-sulfinate (HBPS). We report the crystal structures of BdsA at a resolution of 2.80 Å. BdsA exists as a homotetramer with a dimer-of-dimers configuration in the crystal, and the interaction between E288 and R296 in BdsA is important for tetramer formation. A structural comparison with homologous proteins shows that the orientation and location of the α9-α12 helices in BdsA are closer to those of the closed form than those of the open form in the EDTA monooxygenase EmoA...
February 16, 2017: Proteins
https://www.readbyqxmd.com/read/28205249/exploration-micromechanism-of-vp35-iid-interaction-and-recognition-dsrna-a-molecular-dynamics-simulation
#3
Yan-Jun Zhang, Jing-Na Ding, Hui Zhong, Ju-Guang Han
Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double-stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA-binding activity, and impairs VP35-mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all-atom molecular dynamics (MD) simulation and binding energy calculation...
February 16, 2017: Proteins
https://www.readbyqxmd.com/read/28168856/biophysical-characterization-and-structural-determination-of-the-potent-cytotoxic-psathyrella-asperospora-lectin
#4
João P Ribeiro, Mohamed Ali Abol Hassan, Razina Rouf, Evelin Tiralongo, Tom W May, Christopher J Day, Anne Imberty, Joe Tiralongo, Annabelle Varrot
A lectin with strong cytotoxic effect on human colon cancer HT29 and monkey kidney VERO cells was recently identified from the Australian indigenous mushroom Psathyrella asperospora and named PAL. We herein present its biochemical and structural analysis using a multidisciplinary approach. Glycan arrays revealed binding preference towards N-acetylglucosamine (GlcNAc) and, to a lesser extent, towards sialic acid (Neu5Ac). Submicromolar and millimolar affinity was measured by surface plasmon resonance for GlcNAc and NeuAc, respectively...
February 7, 2017: Proteins
https://www.readbyqxmd.com/read/28168775/structural-characterization-of-the-pts-iia-and-iib-proteins-associated-with-pneumococcal-fucose-utilization
#5
Melanie A Higgins, Aileen M Hamilton, Alisdair B Boraston
Streptococcus pneumoniae harbors a significant number of transporters, including phosphotransferase (PTS) systems, allowing the bacterium to utilize a number of different carbohydrates for metabolic and other purposes. The genes encoding for one PTS transport system in particular (EII(fuc) ) are found within a fucose utilization operon in S. pneumoniae TIGR4. Here, we report the 3-dimensional structures of IIA(fuc) and IIB(fuc) providing evidence that this PTS system belongs to the EII(man) family. Additionally, the predicted metabolic pathway for this distinctive fucose utilization system suggests that EII(fuc) transports the H-disaccharide blood group antigen, which would represent a novel PTS transporter specificity...
February 7, 2017: Proteins
https://www.readbyqxmd.com/read/28168752/monte-carlo-replica-exchange-based-ensemble-docking-of-protein-conformations
#6
Zhe Zhang, Uwe Ehmann, Martin Zacharias
A Replica-exchange Monte Carlo (REMC) ensemble docking approach has been developed that allows efficient exploration of protein-protein docking geometries. In addition to Monte Carlo steps in translation and orientation of binding partners, possible conformational changes upon binding are included based on Monte Carlo selection of protein conformations stored as ordered pre-generated conformational ensembles. The conformational ensembles of each binding partner protein were generated by three different approaches starting from the unbound partner protein structure with a range spanning a root mean square deviation of 1-2...
February 7, 2017: Proteins
https://www.readbyqxmd.com/read/28168746/perspectives-and-expectations-in-structural-bioinformatics-of-metalloproteins
#7
EDITORIAL
Sen Yao, Robert M Flight, Eric C Rouchka, Hunter N B Moseley
Recent papers highlight the presence of large numbers of compressed angles in metal ion coordination geometries for metalloprotein entries in the worldwide Protein Data Bank, due mainly to multidentate coordination. The prevalence of these compressed angles has raised the controversial idea that significantly populated aberrant or even novel coordination geometries may exist. Some of these papers have undergone severe criticism, apparently due to views held that only canonical coordination geometries exist in significant numbers...
February 7, 2017: Proteins
https://www.readbyqxmd.com/read/28168745/the-adaptive-nature-of-protein-residue-networks
#8
Wael I Karain, Nael I Qaraeen
Protein residue networks PRNs are used to describe proteins. These networks are usually based on an average structure for the protein. However, proteins are dynamic entities that are affected by their surroundings. In this work, we study the effect of temperatures above and below the protein dynamical transition temperature(≈200K), on three important network parameters gleaned from weighted PRNs for the solvated β-Lactamase Inhibitory Protein BLIP: the betweenness centrality B, the closeness centrality C, and the clustering coefficient CC...
February 7, 2017: Proteins
https://www.readbyqxmd.com/read/28168743/experimental-conformational-energy-maps-of-proteins-and-peptides
#9
Govardhan A Balaji, H G Nagendra, Vitukudi N Balaji, Shashidhar N Rao
We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F.M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ,ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions...
February 7, 2017: Proteins
https://www.readbyqxmd.com/read/28160322/atlas-a-database-linking-binding-affinities-with-structures-for-wild-type-and-mutant-tcr-pmhc-complexes
#10
Tyler Borrman, Jennifer Cimons, Michael Cosiano, Michael Purcaro, Brian G Pierce, Brian M Baker, Zhiping Weng
The ATLAS (Altered TCR Ligand Affinities and Structures) database (https://zlab.umassmed.edu/atlas/web/ is a manually curated repository containing the binding affinities for wild-type and mutant T cell receptors (TCRs) and their antigens, peptides presented by the major histocompatibility complex (pMHC). The database links experimentally measured binding affinities with the corresponding three dimensional (3D) structures for TCR-pMHC complexes. The user can browse and search affinities, structures, and experimental details for TCRs, peptides, and MHCs of interest...
February 3, 2017: Proteins
https://www.readbyqxmd.com/read/28160315/solution-nmr-structure-of-rhe_ch02687-from-rhizobium-etli-a-novel-flavonoid-binding-protein
#11
Chunjie Liang, Jiang Zhu, Rui Hu, Theresa A Ramelot, Michael A Kennedy, Maili Liu, Yunhuang Yang
We report the solution NMR structure of RHE_CH02687 from Rhizobium etli. Its structure consists of two β-sheets that together with two short and one long α-helix form a hydrophobic cavity. This protein shows a high structural similarity to the prokaryotic protein YndB from Bacillus subtilis, and the eukaryotic protein Aha1. NMR titration experiments confirmed that RHE_CH02687, like its homolog YndB, interacted with flavonoids, giving support for a biological function as a flavonoid sensor in the symbiotic interaction between R...
February 3, 2017: Proteins
https://www.readbyqxmd.com/read/28160313/solution-nmr-structure-of-zinc-finger-4-and-5-from-human-insm1-an-essential-regulator-of-neuroendocrine-differentiation
#12
Jiang Zhu, Huapu Wang, Theresa A Ramelot, Michael A Kennedy, Rui Hu, Xiali Yue, Maili Liu, Yunhuang Yang
Human INSM1 containing five C-terminal C2H2-type zinc fingers (ZFs), is a key regulator of neuroendocrine development. Previous research reported that full-length INSM1 containing all five ZFs recognized a consensus DNA sequence. Structure elucidation of human INSM1 ZFs is currently insufficient to understand the DNA binding mechanism. Herein, we present the solution NMR structure of ZF4-5, in which the two ZFs adopt a head-to-tail arrangement and each ZF features a canonical ββα fold. NMR titrations and isothermal titration calorimetry experiments showed that ZF4-5 binds weakly to the consensus DNA sequence...
February 3, 2017: Proteins
https://www.readbyqxmd.com/read/28142197/crystal-structure-of-%C3%AE-glucosidase-1a-from-thermotoga-neapolitana-and-comparison-of-active-site-mutants-for-hydrolysis-of-flavonoid-glucosides
#13
Tejas S Kulkarni, Samiullah Khan, Rodrigo Villagomez, Tahir Mahmood, Sofia Lindahl, Derek T Logan, Javier A Linares-Pastén, Eva Nordberg Karlsson
The β-glucosidase TnBgl1A catalyses hydrolysis of O-linked terminal β-glycosidic bonds at the non-reducing end of glycosides/oligosaccharides. Enzymes with this specificity have potential in lignocellulose conversion (degrading cellobiose to glucose) and conversion of bioactive flavonoids (modification of glycosylation results in modulation of bioavailability). Previous work has shown TnBgl1A to hydrolyse 3, 4'and 7 glucosylation in flavonoids, and although conversion of 3-glucosylated substrate to aglycone was low, it was improved by mutagenesis of residue N220...
January 31, 2017: Proteins
https://www.readbyqxmd.com/read/28142195/aberrant-coordination-geometries-discovered-in-the-most-abundant-metalloproteins
#14
Sen Yao, Robert M Flight, Eric C Rouchka, Hunter N B Moseley
Metalloproteins bind and utilize metal ions for a variety of biological purposes. Due to the ubiquity of metalloprotein involvement throughout these processes across all domains of life, how proteins coordinate metal ions for different biochemical functions is of great relevance to understanding the implementation of these biological processes. Towards these ends, we have improved our methodology for structurally and functionally characterizing metal binding sites in metalloproteins. Our new ligand detection method is statistically much more robust, producing estimated false positive and false negative rates of ∼0...
January 31, 2017: Proteins
https://www.readbyqxmd.com/read/28120530/thermodynamic-and-structural-effect-of-urea-and-guanidine-chloride-on-the-helical-and-on-a-hairpin-fragment-of-gb1-from-molecular-simulations
#15
R Meloni, G Tiana
With the help of molecular-dynamics simulations, we studied the effect of urea and guanidine chloride on the thermodynamic and structural properties of the helical fragment of protein GB1, comparing them with those of its second beta hairpin. We showed that the helical fragment in different solvents populates an ensemble of states that is more complex than that of the hairpin, and thus the associated experimental observables (circular-dichroism spectra, secondary chemical shifts, m values), that we back-calculated from the simulations and compared with the actual data, are more difficult to interpret...
January 25, 2017: Proteins
https://www.readbyqxmd.com/read/28120477/discovery-of-rab1-binding-sites-using-an-ensemble-of-clustering-methods
#16
Suryani Lukman, Minh N Nguyen, Kelvin Sim, Jeremy C M Teo
Targeting non-native-ligand binding sites for potential investigative and therapeutic applications is an attractive strategy in proteins that share common native ligands, as in Rab1 protein. Rab1 is a subfamily member of Rab proteins, which are members of Ras GTPase superfamily. All Ras GTPase superfamily members bind to native ligands GTP and GDP, that switch on and off the proteins, respectively. Rab1 is physiologically essential for autophagy and transport between endoplasmic reticulum and Golgi apparatus...
January 25, 2017: Proteins
https://www.readbyqxmd.com/read/28120439/multiple-helical-conformations-of-the-helix-turn-helix-region-revealed-by-noe-restrained-md-simulations-of-tryptophan-aporepressor-trpr
#17
Balasubramanian Harish, G V T Swapna, Gregory J Kornhaber, Gaetano T Montelione, Jannette Carey
The nature of flexibility in the helix-turn-helix region of E. coli trp aporepressor has been unexplained for many years. The original ensemble of NMR structures showed apparent disorder, but chemical shift and relaxation measurements indicated a helical region. NOE data for a temperature-sensitive mutant showed more helical character in its helix-turn-helix region, but nevertheless also led to an apparently disordered ensemble. However, conventional NMR structure determination methods require all structures in the ensemble to be consistent with every NOE simultaneously...
January 25, 2017: Proteins
https://www.readbyqxmd.com/read/28120375/a-combinatorial-scoring-function-for-protein-rna-docking
#18
Zhao Zhang, Lin Lu, Yue Zhang, Chun Hua Li, Cun Xin Wang, Xiao Yi Zhang, Jian Jun Tan
Protein-RNA docking is still an open question. One of the main challenges is to develop an effective scoring function that can discriminate near-native structures from the incorrect ones. To solve the problem, we have constructed a knowledge-based residue-nucleotide pairwise potential with secondary structure information considered for nonribosomal protein-RNA docking. Here we developed a weighted combined scoring function RpveScore that consists of the pairwise potential and six physics-based energy terms...
January 25, 2017: Proteins
https://www.readbyqxmd.com/read/28120429/structural-insights-into-human-microsomal-epoxide-hydrolase-by-combined-homology-modeling-molecular-dynamics-simulations-and-molecular-docking-calculations
#19
Patricia Saenz-Méndez, Aline Katz, María Lucía Pérez-Kempner, Oscar N Ventura, Marta Vázquez
A new homology model of human microsomal epoxide hydrolase was derived based on multiple templates. The model obtained was fully evaluated, including MD simulations and ensemble-based docking, showing that the quality of the structure is better than that of only previously known model. Particularly, a catalytic triad was clearly identified, in agreement with the experimental information available. Analysis of intermediates in the enzymatic mechanism led to the identification of key residues for substrate binding, stereoselectivity, and intermediate stabilization during the reaction...
January 24, 2017: Proteins
https://www.readbyqxmd.com/read/28106297/different-dynamics-and-pathway-of-disulfide-bonds-reduction-of-two-human-defensins-a-molecular-dynamics-simulation-study
#20
Liqun Zhang
Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5(HD5) and human β defensin type 3 (hBD-3) have 6 cysteine residues which form 3 pairs of disulfide bonds under oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order has been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD-3 wildtype and analogs which have all 3 disulfide bonds released under reducing conditions...
January 20, 2017: Proteins
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