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Protein structure prediction

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https://www.readbyqxmd.com/read/28214450/in-silico-structural-and-functional-analysis-of-mesorhizobium-acc-deaminase
#1
Krishnendu Pramanik, Tithi Soren, Soumik Mitra, Tushar Kanti Maiti
Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of biotic or abiotic stresses. 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase is a rhizobial enzyme which cleaves ACC (immediate precursor of ethylene) into α-ketobutyrate and ammonia. As a result, the level of ethylene from the plant cells is decreased and the negative impact of ethylene on nodule formation is reduced...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28213174/evidence-of-the-presence-of-a-calmodulin-sensitive-plasma-membrane-ca-2-atpase-in-trypanosoma-equiperdum
#2
María Carolina Pérez-Gordones, José Rubén Ramírez-Iglesias, Vincenza Cervino, Graciela L Uzcanga, Gustavo Benaim, Marta Mendoza
Trypanosoma equiperdum belongs to the subgenus Trypanozoon, which has a significant socio-economic impact by limiting animal protein productivity worldwide. Proteins involved in the intracellular Ca(2+) regulation are prospective chemotherapeutic targets since several drugs used in experimental treatment against trypanosomatids exert their action through the disruption of the parasite intracellular Ca(2+) homeostasis. Therefore, the plasma membrane Ca(2+)-ATPase (PMCA) is considered as a potential drug target...
February 14, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28212856/probis-tools-algorithm-database-and-web-servers-for-predicting-and-modeling-of-biologically-interesting-proteins
#3
REVIEW
Janez Konc, Dušanka Janežič
ProBiS (Protein Binding Sites) Tools consist of algorithm, database, and web servers for prediction of binding sites and protein ligands based on the detection of structurally similar binding sites in the Protein Data Bank. In this article, we review the operations that ProBiS Tools perform, provide comments on the evolution of the tools, and give some implementation details. We review some of its applications to biologically interesting proteins. ProBiS Tools are freely available at http://probis.cmm.ki.si and http://probis...
February 14, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28212855/depth-dependent-amino-acid-substitution-matrices-and-its-use-in-predicting-deleterious-mutations
#4
REVIEW
Nida Farheen, Neeladri Sen, Sanjana Nair, Kuan Pern Tan, M S Madhusudhan
The 20 naturally occurring amino acids have different environmental preferences of where they are likely to occur in protein structures. Environments in a protein can be classified by their proximity to solvent by the residue depth measure. Since the frequencies of amino acids are different at various depth levels, the substitution frequencies should vary according to depth. To quantify these substitution frequencies, we built depth dependent substitution matrices. The dataset used for creation of the matrices consisted of 3696 high quality, non redundant pairwise protein structural alignments...
February 14, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28211907/identification-of-extracellular-segments-by-mass-spectrometry-improves-topology-prediction-of-transmembrane-proteins
#5
Tamás Langó, Gergely Róna, Éva Hunyadi-Gulyás, Lilla Turiák, Julia Varga, László Dobson, György Várady, László Drahos, Beáta G Vértessy, Katalin F Medzihradszky, Gergely Szakács, Gábor E Tusnády
Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210877/quantum-mechanical-treatment-of-as-3-thiol-model-compounds-implication-for-the-core-structure-of-as-iii-metallothionein
#6
Roobee Garla, Narinder Kaur, Mohinder Pal Bansal, Mohan Lal Garg, Biraja Prasad Mohanty
Exposure to inorganic arsenic (As) is one of the major health concerns in several regions around the world. Binding of As(III) with thiols is central to the mechanisms related to its toxicity, detoxification, and therapeutic effects. Due to its high thiol content, metallothionein (MT) is presumed to play an important role in case of arsenic toxicity. Consequences of these As-thiol interactions are not yet clear due to various difficulties in the characterization of arsenic bound proteins by spectroscopic techniques...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28209133/house-spider-genome-uncovers-evolutionary-shifts-in-the-diversity-and-expression-of-black-widow-venom-proteins-associated-with-extreme-toxicity
#7
Kerry L Gendreau, Robert A Haney, Evelyn E Schwager, Torsten Wierschin, Mario Stanke, Stephen Richards, Jessica E Garb
BACKGROUND: Black widow spiders are infamous for their neurotoxic venom, which can cause extreme and long-lasting pain. This unusual venom is dominated by latrotoxins and latrodectins, two protein families virtually unknown outside of the black widow genus Latrodectus, that are difficult to study given the paucity of spider genomes. Using tissue-, sex- and stage-specific expression data, we analyzed the recently sequenced genome of the house spider (Parasteatoda tepidariorum), a close relative of black widows, to investigate latrotoxin and latrodectin diversity, expression and evolution...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28208298/surface-accessibility-and-dynamics-of-macromolecular-assemblies-probed-by-covalent-labeling-mass-spectrometry-and-integrative-modeling
#8
Carla Schmidt, Jamie A Macpherson, Andy M Lau, Ken Wei Tan, Franca Fraternali, Argyris Politis
Mass spectrometry (MS) has become an indispensable tool for investigating the architectures and dynamics of macromolecular assemblies. Here we show that covalent labeling of solvent accessible residues followed by their MS-based identification yields modeling restraints that allow mapping the location and orientation of subunits within protein assemblies. Together with complementary restraints derived from cross-linking and native MS, we built native-like models of four heterocomplexes with known subunit structures and compared them with available X-ray crystal structures...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28208072/identification-of-triosephosphate-isomerase-as-a-novel-allergen-in-octopus-fangsiao
#9
Yang Yang, Zhong-Wei Chen, Barry K Hurlburt, Gui-Ling Li, Yong-Xia Zhang, Dan-Xia Fei, Hai-Wang Shen, Min-Jie Cao, Guang-Ming Liu
Octopus is an important mollusk in human dietary for its nutritional value, however it also causes allergic reactions in humans. Major allergens from octopus have been identified, while the knowledge of novel allergens remains poor. In the present study, a novel allergen with molecular weight of 28kDa protein was purified from octopus (Octopus fangsiao) and identified as triosephosphate isomerase (TIM) by mass spectrometry. TIM aggregated beyond 45°C, and its IgE-binding activity was affected under extreme pH conditions due to the altered secondary structure...
February 13, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28207756/structural-changes-on-a-molecular-basis-of-canola-meal-by-conditioning-temperature-and-time-during-pelleting-process-in-relation-to-physiochemical-energy-and-protein-properties-relevant-to-ruminants
#10
Xuewei Huang, Huihua Zhang, Peiqiang Yu
The objectives of this study were: (1) To investigate the effects of conditioning temperature (70, 80, 90°C), time (30, 60 sec), and interaction (temperature × time) during the pelleting process on internal protein molecular structure changes of the co-products; (2) To identify differences in protein molecular structures among pellets that were processed under different conditions, and between unprocessed mash and pellets; 3) To quantify protein molecular structure changes in relation to predicted energy and protein utilization in dairy cows...
2017: PloS One
https://www.readbyqxmd.com/read/28205569/heteroaryldihydropyrimidine-hap-and-sulfamoylbenzamide-sba-inhibit-hepatitis-b-virus-replication-by-different-molecular-mechanisms
#11
Zheng Zhou, Taishan Hu, Xue Zhou, Steffen Wildum, Fernando Garcia-Alcalde, Zhiheng Xu, Daitze Wu, Yi Mao, Xiaojun Tian, Yuan Zhou, Fang Shen, Zhisen Zhang, Guozhi Tang, Isabel Najera, Guang Yang, Hong C Shen, John A T Young, Ning Qin
Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205163/hybrid-in-silico-in-vitro-approaches-for-the-identification-of-functional-cholesterol-binding-domains-in-membrane-proteins
#12
Coralie Di Scala, Jacques Fantini
In eukaryotic cells, cholesterol is an important regulator of a broad range of membrane proteins, including receptors, transporters, and ion channels. Understanding how cholesterol interacts with membrane proteins is a difficult task because structural data of these proteins complexed with cholesterol are scarce. Here, we describe a dual approach based on in silico studies of protein-cholesterol interactions, combined with physico-chemical measurements of protein insertion into cholesterol-containing monolayers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28202679/from-molecular-chaperones-to-membrane-motors-through-the-lens-of-a-mass-spectrometrist
#13
REVIEW
Carol V Robinson
Twenty-five years ago, we obtained our first mass spectra of molecular chaperones in complex with protein ligands and entered a new field of gas-phase structural biology. It is perhaps now time to pause and reflect, and to ask how many of our initial structure predictions and models derived from mass spectrometry (MS) datasets were correct. With recent advances in structure determination, many of the most challenging complexes that we studied over the years have become tractable by other structural biology approaches enabling such comparisons to be made...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28202413/engineered-antibody-ch2-domains-binding-to-nucleolin-isolation-characterization-and-improvement-of-aggregation
#14
De-Zhi Li, Rui Gong, Jun Zheng, Xi-Hai Chen, Dimiter S Dimitrov, Qi Zhao
Smaller recombinant antibody fragments are now emerging as alternatives of conventional antibodies. Especially, immunoglobulin (Ig) constant CH2 domain and engineered CH2 with improved stability are promising as scaffolds for selection of specific binders to various antigens. We constructed a yeast display library based on an engineered human IgG1 CH2 scaffold with diversified loop regions. A group of CH2 binders were isolated from this yeast display library by panning against nucleolin, which is a tumor-associated antigen involved in cell proliferation, tumor cell growth and angiogenesis...
February 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28199368/secondary-structure-prediction-revisited-theoretical-%C3%AE-sheet-propensity-and-coil-propensity-represent-structures-of-amyloids-and-aid-in-elucidating-phenomena-involved-in-interspecies-transmission-of-prions
#15
Yuzuru Taguchi, Noriyuki Nishida
Prions are unique infectious agents, consisting solely of abnormally-folded prion protein (PrPSc). However, they possess virus-like features, including strain diversity, the ability to adapt to new hosts and to be altered evolutionarily. Because prions lack genetic material (DNA and RNA), these biological phenomena have been attributed to the structural properties of PrPSc. Therefore, many structural models of the structure of PrPSc have been proposed based on the limited structural information available, regardless of the incompatibility with high-resolution structural analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28196882/trade-offs-between-enzyme-fitness-and-solubility-illuminated-by-deep-mutational-scanning
#16
Justin R Klesmith, John-Paul Bacik, Emily E Wrenbeck, Ryszard Michalczyk, Timothy A Whitehead
Proteins are marginally stable, and an understanding of the sequence determinants for improved protein solubility is highly desired. For enzymes, it is well known that many mutations that increase protein solubility decrease catalytic activity. These competing effects frustrate efforts to design and engineer stable, active enzymes without laborious high-throughput activity screens. To address the trade-off between enzyme solubility and activity, we performed deep mutational scanning using two different screens/selections that purport to gauge protein solubility for two full-length enzymes...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28196871/identification-of-a-transcriptional-activation-domain-in-yeast-repressor-activator-protein-1-rap1-using-an-altered-dna-binding-specificity-variant
#17
Amanda N Johnson, P Anthony Weil
Repressor Activator Protein 1 (Rap1) performs multiple vital cellular functions in the budding yeast Saccharomyces cerevisiae. These include regulation of telomere length, transcriptional repression of both telomere-proximal genes and the silent mating type loci, and transcriptional activation of hundreds of mRNA-encoding genes, including the highly transcribed ribosomal protein- and glycolytic enzyme-encoding genes. Studies of the contributions of Rap1 to telomere length regulation and transcriptional repression have yielded significant mechanistic insights...
February 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28196677/molecular-modeling-docking-and-dynamics-simulations-of-the-dioclea-lasiophylla-mart-ex-benth-seed-lectin-an-edematogenic-and-hypernociceptive-protein
#18
Vanir Reis Pinto-Junior, Vinicius Jose Silva Osterne, Mayara Queiroz Santiago, Claudia Figueiredo Lossio, Celso Shiniti Nagano, Cintia Renata Costa Rocha, Jessica Catarine Frutuoso Nascimento, Francisco Lucas Faustino Nascimento, Ivanice Bezerra Silva, Antonia Simoni Oliveira, Jorge Luis Almeida Correia, Rodrigo Bainy Leal, Ana Maria Sampaio Assreuy, Benildo Sousa Cavada, Kyria Santiago Nascimento
Lectins are proteins, or glycoproteins, capable of reversibly binding to specific mono- or oligosaccharides via a noncatalytic domain. The Diocleinae subtribe presents lectins with high structural similarity, but different effects based on biological activity assays. This variability results from small structural differences. Therefore, in this context, the present study aimed to perform a structural analysis of the lectin from Dioclea lasiophylla Mart. ex Benth seeds (DlyL) and evaluate its inflammatory effect...
February 11, 2017: Biochimie
https://www.readbyqxmd.com/read/28195698/structure-based-targeting-of-orthologous-pathogen-proteins-accelerates-anti-parasitic-drug-discovery
#19
Vitul Jain, Arvind Sharma, Gajinder Pal Singh, Manickam Yogavel, Amit Sharma
Parasitic diseases caused by eukaryotic pathogens impose significant health and economic burden worldwide. The level of research funding available for many parasitic diseases is insufficient in relation to their adverse social impact. Here, we review the extant 3D structural data on protein-inhibitor complexes that can be harnessed to accelerate drug discovery against many related pathogens. Assessment of sequence conservation within drug/inhibitor-binding residues in enzyme-inhibitor complexes can be leveraged to predict and validate both new lead compounds and their molecular targets in multiple parasitic diseases...
February 14, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28194972/fragment-based-approach-for-the-evaluation-of-nmr-chemical-shifts-for-large-biomolecules-incorporating-the-effects-of-the-solvent-environment
#20
K V Jovan Jose, Krishnan Raghavachari
We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large biomolecules. Density functional techniques have been employed in conjunction with large basis sets and including the effects of the solvent environment in these calculations. The MIM-NMR method is initially benchmarked on a set of (alanine)10 conformers containing strong intramolecular interactions. The incorporation of a second low level of theory to recover the missing long-range interactions in the primary fragmentation scheme is critical to yield reliable chemical shifts, with a mean absolute deviation (MAD) from direct unfragmented calculations of 0...
February 14, 2017: Journal of Chemical Theory and Computation
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