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Protein structure alignment

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https://www.readbyqxmd.com/read/27917435/analysis-of-the-ionic-interaction-between-the-hydrophobin-roda-and-two-cutinases-of-aspergillus-nidulans-obtained-via-an-aspergillus-oryzae-expression-system
#1
Takumi Tanaka, Mayumi Nakayama, Toru Takahashi, Kei Nanatani, Youhei Yamagata, Keietsu Abe
Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. In the fungus Aspergillus oryzae, the hydrophobin RolA and the polyesterase CutL1 are co-expressed when the sole available carbon source is the biodegradable polyester polybutylene succinate-co-adipate (PBSA). RolA promotes the degradation of PBSA by attaching to the particle surface, changing its structure and interacting with CutL1 to concentrate CutL1 on the PBSA surface. We previously reported that positively charged residues in RolA and negatively charged residues in CutL1 are cooperatively involved in the ionic interaction between RolA and CutL1...
December 5, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27914300/structure-based-analysis-of-bacilli-and-plasmid-dihydrofolate-reductase-evolution
#2
Mona Alotaibi, Ben Delos Reyes, Tin Le, Phuong Luong, Faramarz Valafar, Robert P Metzger, Gary B Fogel, David Hecht
Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database...
November 22, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27911737/the-conservation-of-phosphate-binding-residues-among-pht1-transporters-suggests-that-distinct-transport-affinities-are-unlikely-to-result-from-differences-in-the-phosphate-binding-site
#3
REVIEW
S Antony Ceasar, Alison Baker, Stephen P Muench, S Ignacimuthu, Stephen A Baldwin
The plant PHosphate Transporter 1 (PHT1) family of membrane proteins belongs to the major facilitator super family and plays a major role in the acquisition of inorganic phosphate (Pi) from the soil and its transport within the plant. These transporters have been well characterized for expression patterns, localization, and in some cases affinity. Furthermore, the crystal structure of a high-affinity eukaryotic phosphate transporter from the fungus Piriformospora indica (PiPT) has revealed important information on the residues involved in Pi transport...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27908666/molecular-cloning-and-expression-analysis-of-five-heat-shock-protein-70-hsp70-family-members-in-lateolabrax-maculatus-with-vibrio-harveyi-infection
#4
Ying-Li Han, Cong-Cong Hou, Chen Du, Jun-Quan Zhu
Heat shock proteins 70 (HSP70s) are molecular chaperones that aid in protection against environmental stress. In this study, we cloned and characterized five members of the HSP70 family (designated as HSPa1a, HSC70-1, HSC70-2, HSPa4 and HSPa14) from Lateolabrax maculatus using rapid amplification cDNA ends (RACE). Multiple sequence alignment and structural analysis revealed that all members of the HSP70 family had a conserved domain architecture, with some distinguishing features unique to each HSP70. Quantitative real-time (qPCR) analysis revealed that all members of the HSP70 family were ubiquitously and differentially expressed in all major types of tissues, including testicular tissue...
November 28, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27907864/heterolytic-oo-bond-cleavage-functional-role-of-glu113-during-bis-fe-iv-formation-in-maug
#5
Jiafeng Geng, Lu Huo, Aimin Liu
The diheme enzyme MauG utilizes H2O2 to perform oxidative posttranslational modification on a protein substrate. A bis-Fe(IV) species of MauG was previously identified as a key intermediate in this reaction. Heterolytic cleavage of the OO bond of H2O2 drives the formation of the bis-Fe(IV) intermediate. In this work, we tested a hypothesis that a glutamate residue, Glu113 in the distal pocket of the pentacoordinate heme of MauG, facilitates heterolytic OO bond cleavage, thereby leading to bis-Fe(IV) formation...
November 9, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/27907154/pheromone-recognition-and-selectivity-by-comr-proteins-among-streptococcus-species
#6
Erin Shanker, Donald A Morrison, Antoine Talagas, Sylvie Nessler, Michael J Federle, Gerd Prehna
Natural transformation, or competence, is an ability inherent to bacteria for the uptake of extracellular DNA. This process is central to bacterial evolution and allows for the rapid acquirement of new traits, such as antibiotic resistance in pathogenic microorganisms. For the Gram-positive bacteria genus Streptococcus, genes required for competence are under the regulation of quorum sensing (QS) mediated by peptide pheromones. One such system, ComRS, consists of a peptide (ComS) that is processed (XIP), secreted, and later imported into the cytoplasm, where it binds and activates the transcription factor ComR...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27901124/analysis-of-chikungunya-virus-proteins-reveals-that-non-structural-proteins-nsp2-and-nsp3-exhibit-rna-interference-rnai-suppressor-activity
#7
Kalika Mathur, Abhishek Anand, Sunil Kumar Dubey, Neeti Sanan-Mishra, Raj K Bhatnagar, Sujatha Sunil
RNAi pathway is an antiviral defence mechanism employed by insects that result in degradation of viral RNA thereby curbing infection. Several viruses including flaviviruses encode viral suppressors of RNAi (VSRs) to counteract the antiviral RNAi pathway. Till date, no VSR has been reported in alphaviruses. The present study was undertaken to evaluate chikungunya virus (CHIKV) proteins for RNAi suppressor activity. We systematically analyzed all nine CHIKV proteins for RNAi suppressor activity using Sf21 RNAi sensor cell line based assay...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900841/the-role-of-the-prod1-membrane-anchor-in-newt-limb-regeneration
#8
Kaoru Nomura, Yasushi Tanimoto, Fumio Hayashi, Erisa Harada, Xiao-Yuan Shan, Masafumi Shionyu, Atsushi Hijikata, Tsuyoshi Shirai, Kenichi Morigaki, Keiko Shimamoto
Prod1 is a protein that regulates limb regeneration in salamanders by determining the direction of limb growth. Prod1 is attached to the membrane by a glycosylphosphatidylinositol (GPI) anchor, but the role of membrane anchoring in the limb regeneration process is poorly understood. In this study, we investigated the functional role of the anchoring of Prod1 to the membrane by using its synthetic mimics in combination with solid-state NMR spectroscopy and fluorescent microscopy techniques. Anchoring did not affect the three-dimensional structure of Prod1 but did induce aggregation by aligning the molecules and drastically reducing the molecular motion on the two-dimensional membrane surface...
November 30, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27900493/mining-the-cicer-arietinum-genome-for-the-mildew-locus-o-mlo-gene-family-and-comparative-evolutionary-analysis-of-the-mlo-genes-from-medicago-truncatula-and-some-other-plant-species
#9
Reena Deshmukh, V K Singh, Brahma Deo Singh
The mildew locus O (Mlo) gene family is ubiquitous in land plants. Some members of this gene family are involved in negative regulation of powdery mildew resistance, while others are involved in several other biological functions. Mlo proteins have characteristic seven transmembrane domains and a calmodulin-binding domain at their C-termini, and are associated with plasma membrane. The Mlo gene family has been studied in several economically important cereals, but little information is available on this gene family in the important legumes, Medicago truncatula Gaertn...
November 30, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27899584/cath-an-expanded-resource-to-predict-protein-function-through-structure-and-sequence
#10
Natalie L Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, David Lee, Paul Ashford, Christine A Orengo, Ian Sillitoe
The latest version of the CATH-Gene3D protein structure classification database has recently been released (version 4.1, http://www.cathdb.info). The resource comprises over 300 000 domain structures and over 53 million protein domains classified into 2737 homologous superfamilies, doubling the number of predicted protein domains in the previous version. The daily-updated CATH-B, which contains our very latest domain assignment data, provides putative classifications for over 100 000 additional protein domains...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899282/bindprofx-assessing-mutation-induced-binding-affinity-change-by-protein-interface-profiles-with-pseudo-counts
#11
Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang
Understanding how gene-level mutations affect the binding affinity of protein-protein interactions is a key issue of protein engineering. Due to the complexity of the problem, using physical force field to predict the mutation-induced binding free-energy change remains challenging. In this work, we present a renewed approach to calculate the impact of gene mutations on the binding affinity through the structure-based profiling of protein-protein interfaces, where the binding free-energy change (ΔΔG) is counted as the logarithm of relative probability of mutant amino acids over wild-type ones in the interface alignment matrix; three pseudo counts are introduced to alleviate the limit of the current interface library...
November 26, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27898663/as-simple-as-possible-but-not-simpler-exploring-the-fidelity-of-coarse-grained-protein-models-for-simulated-force-spectroscopy
#12
Mona Habibi, Jörg Rottler, Steven S Plotkin
Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō)...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27896723/large-scale-sequence-comparison
#13
Devi Lal, Mansi Verma
There are millions of sequences deposited in genomic databases, and it is an important task to categorize them according to their structural and functional roles. Sequence comparison is a prerequisite for proper categorization of both DNA and protein sequences, and helps in assigning a putative or hypothetical structure and function to a given sequence. There are various methods available for comparing sequences, alignment being first and foremost for sequences with a small number of base pairs as well as for large-scale genome comparison...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896722/multiple-sequence-alignment
#14
Punto Bawono, Maurits Dijkstra, Walter Pirovano, Anton Feenstra, Sanne Abeln, Jaap Heringa
The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. Significant advances have been achieved in this field, and many useful tools have been developed for constructing alignments, although many biological and methodological issues are still open...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895624/visualizing-evolutionary-relationships-of-multidomain-proteins-an-example-from-receiver-rec-domains-of-sensor-histidine-kinases-in-the-candidatus-maribeggiatoa-str-orange-guaymas-draft-genome
#15
Barbara J MacGregor
For multidomain proteins, evolutionary changes may occur at the domain as well as the whole-protein level. An example is presented here, with suggestions for how such complicated relationships might be visualized. Earlier analysis of the Candidatus Maribeggiatoa str. Orange Guaymas (BOGUAY; Gammaproteobacteria) single-filament draft genome found evidence of gene exchange with the phylogenetically distant Cyanobacteria, particularly for sensory and signal transduction proteins. Because these are modular proteins, known to undergo frequent duplication, domain swapping, and horizontal gene transfer, a single domain was chosen for analysis...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27891772/twoplex-12-13-c6-aniline-stable-isotope-and-linkage-specific-sialic-acid-labelling-2d-lc-ms-workflow-for-quantitative-n-glycomics
#16
Simone Albrecht, Stefan Mittermayr, Josh Smith, Silvia Millán Martín, Margaret Doherty, Jonathan Bones
Quantitative glycomics represents an actively expanding research field ranging from the discovery of disease associated glycan alterations to the quantitative characterization of N-glycans on therapeutic proteins. Commonly used analytical platforms for comparative relative quantitation of complex glycan samples include MALDI-ToF-MS or chromatographic glycan profiling with subsequent data alignment and statistical evaluation. Limitations of such approaches include run-to-run technical variation and the potential introduction of subjectivity during data processing...
November 28, 2016: Proteomics
https://www.readbyqxmd.com/read/27890086/multiple-isoforms-for-the-catalytic-subunit-of-pka-in-the-basal-fungal-lineage-mucor-circinelloides
#17
Lucas Fernández Núñez, Josefina Ocampo, Alexandra M Gottlieb, Silvia Rossi, Silvia Moreno
Protein kinase A (PKA) activity is involved in dimorphism of the basal fungal lineage Mucor. From the recently sequenced genome of Mucor circinelloides we could predict ten catalytic subunits of PKA. From sequence alignment and structural prediction we conclude that the catalytic core of the isoforms is conserved, and the difference between them resides in their amino termini. This high number of isoforms is maintained in the subdivision Mucoromycotina. Each paralogue, when compared to the ones form other fungi is more homologous to one of its orthologs than to its paralogs...
December 2016: Fungal Biology
https://www.readbyqxmd.com/read/27886223/redox-cofactors-insertion-in-prokaryotic-molybdoenzymes-occurs-via-a-conserved-folding-mechanism
#18
Rodrigo Arias-Cartin, Pierre Ceccaldi, Barbara Schoepp-Cothenet, Klaudia Frick, Jean-Michel Blanc, Bruno Guigliarelli, Anne Walburger, Stéphane Grimaldi, Thorsten Friedrich, Véronique Receveur-Brechot, Axel Magalon
A major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. This holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. This large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (Mo/W-bisPGD) and Fe/S clusters. Here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational changes accompanying Mo/W-bisPGD and Fe/S cofactors insertion...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27882067/bioinformatic-identification-of-rare-codon-clusters-rccs-in-hbv-genome-and-evaluation-of-rccs-in-proteins-structure-of-hepatitis-b-virus
#19
Mojtaba Mortazavi, Mohammad Zarenezhad, Saeid Gholamzadeh, Seyed Moayed Alavian, Mohammad Ghorbani, Reza Dehghani, Abdorrasoul Malekpour, Mohammadhasan Meshkibaf, Ali Fakhrzad
BACKGROUND: Hepatitis B virus (HBV) as an infectious disease that has nine genotypes (A - I) and a 'putative' genotype J. OBJECTIVES: The aim of this study was to identify the rare codon clusters (RCC) in the HBV genome and to evaluate these RCCs in the HBV proteins structure. METHODS: For detection of protein family accession numbers (Pfam) in HBV proteins, the UniProt database and Pfam search tool were used. Protein family accession numbers is a comprehensive and accurate collection of protein domains and families...
October 2016: Hepatitis Monthly
https://www.readbyqxmd.com/read/27881430/a-comprehensive-review-and-comparison-of-different-computational-methods-for-protein-remote-homology-detection
#20
Junjie Chen, Mingyue Guo, Xiaolong Wang, Bin Liu
Protein remote homology detection is one of the most fundamental and central problems for the studies of protein structures and functions, aiming to detect the distantly evolutionary relationships among proteins via computational methods. During the past decades, many computational approaches have been proposed to solve this important task. These methods have made a substantial contribution to protein remote homology detection. Therefore, it is necessary to give a comprehensive review and comparison on these computational methods...
November 22, 2016: Briefings in Bioinformatics
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