keyword
MENU ▼
Read by QxMD icon Read
search

Protein structure alignment

keyword
https://www.readbyqxmd.com/read/28650167/molecular-insight-into-the-adsorption-of-spruce-budworm-antifreeze-protein-to-ice-surface-a-clathrate-mediated-recognition-mechanism
#1
Sandipan Chakraborty, Biman Jana
The principal mechanism of ice recognition by antifreeze protein (AFP) is a topic of intense discussion in recent times. Despite of many experimental and theoretical studies, the detailed understanding of the process remains elusive. Present work aims to explore the molecular mechanism of ice recognition by an insect AFP from Spruce budworm, sbwAFP. Evident from our simulation, water dynamics becomes highly sluggish around the IBS due to the combined effect of confinement and ordering induced by the perfectly aligned methyl side-chains of threonine residues, the THRs ladder...
June 26, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28648607/crystal-structure-of-chicken-%C3%AE-s-crystallin-reveals-lattice-contacts-with-implications-for-function-in-the-lens-and-the-evolution-of-the-%C3%AE-%C3%AE-crystallins
#2
Vatsala Sagar, Sumit K Chaturvedi, Peter Schuck, Graeme Wistow
Previous attempts to crystallize mammalian γS-crystallin were unsuccessful. Native L16 chicken γS crystallized avidly while the Q16 mutant did not. The X-ray structure for chicken γS at 2.3 Å resolution shows the canonical structure of the superfamily plus a well-ordered N arm aligned with a β sheet of a neighboring N domain. L16 is also in a lattice contact, partially shielded from solvent. Unexpectedly, the major lattice contact matches a conserved interface (QR) in the multimeric β-crystallins. QR shows little conservation of residue contacts, except for one between symmetry-related tyrosines, but molecular dipoles for the proteins with QR show striking similarities while other γ-crystallins differ...
June 9, 2017: Structure
https://www.readbyqxmd.com/read/28632082/the-%C3%AE-helix-alignment-of-proteins-in-water-solution-toward-a-high-frequency-electromagnetic-field-a-ftir-spectroscopy-study
#3
Emanuele Calabrò, Salvatore Magazù
The aim of this article was to study the effects of mobile phone electromagnetic waves at 1750 MHz on the Amide I and Amide II vibration bands of some proteins in bidistilled water solution by means of Fourier transform infrared (FTIR) spectroscopy and Fourier self-deconvolution (FSD) analysis. The proteins that were used for the experiment were hemoglobin, myoglobin, bovine serum albumin and lysozyme. The exposure system consisted of microwaves emitted by an operational mobile phone at the frequency at 1750 MHz at the average power density of 1 W/m(2)...
June 20, 2017: Electromagnetic Biology and Medicine
https://www.readbyqxmd.com/read/28629383/epitope-mapping-and-characterization-of-a-novel-nsp10-specific-monoclonal-antibody-that-differentiates-genotype-2-prrsv-from-genotype-1-prrsv
#4
Zhibang Zhang, Xuexia Wen, Jianguo Dong, Xinna Ge, Lei Zhou, Hanchun Yang, Xin Guo
BACKGROUND: Porcine reproductive and respiratory syndrome virus (PRRSV), the causative agent of PRRS, has two distinct and highly diverse genotypes (genotype 1 and genotype 2) in the field. Accurate diagnosis and differentiation of the two genotypes of PRRSV are critical to the effective prevention and control of PRRS. The non-structural protein 10 (Nsp10) plays a vital role in viral replication and is one of the most conserved proteins of PRRSV, thus constituting a good candidate for PRRSV diagnosis...
June 19, 2017: Virology Journal
https://www.readbyqxmd.com/read/28629184/determination-of-structural-requirements-of-n-substituted-tetrahydro-%C3%AE-carboline-imidazolium-salt-derivatives-using-in-silico-approaches-for-designing-mek-1-inhibitors
#5
Jingwei Liang, Mingyang Wang, Xinyang Li, Xin He, Chong Cao, Fanhao Meng
Novel N-substituted tetrahydro-β-carboline imidazolium salt derivatives proved to have potent antitumor activity in past research. The Topomer CoMFA and CoMSIA function in Sybyl-X 2.0 software was applied for the identification of important features of N-substituted tetrahydro-β-carboline-imidazolium salt derivative moieties. In the case of Topomer CoMFA, all the compounds were split into two fragments which were used to generate a 3D invariant representation, the statistical results of the Topomer CoMFA model: q² value of 0...
June 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28621916/construction-of-anterior-hemi-corneal-equivalents-using-nontransfected-human-corneal-cells-and-transplantation-in-dog-models
#6
Bin Xu, Zhan Song, Tingjun Fan
Tissue-engineered human anterior hemi-cornea (TE-aHC) is a promising equivalent for treating anterior lamellar keratopathy to surmount the severe shortage of donated corneas. This study was intended to construct a functional TE-aHC with nontransfected human corneal stromal (ntHCS) and epithelial (ntHCEP) cells using acellular porcine corneal stromata (aPCS) as a carrier scaffold, and evaluate its biological functions in a dog model. To construct a TE-aHC, ntHCS cells were injected into an aPCS scaffold and cultured for 3 days; then, ntHCEP cells were inoculated onto the Bowman's membrane of the scaffold and cultured for 5 days under air-liquid interface condition...
June 16, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28616799/dolichol-phosphate-mannose-synthase-a-glycosyltransferase-with-unity-in-molecular-diversities
#7
REVIEW
Dipak K Banerjee, Zhenbo Zhang, Krishna Baksi, Jesús E Serrano-Negrón
N-glycans provide structural and functional stability to asparagine-linked (N-linked) glycoproteins, and add flexibility. Glycan biosynthesis is elaborative, multi-compartmental and involves many glycosyltransferases. Failure to assemble N-glycans leads to phenotypic changes developing infection, cancer, congenital disorders of glycosylation (CDGs) among others. Biosynthesis of N-glycans begins at the endoplasmic reticulum (ER) with the assembly of dolichol-linked tetra-decasaccharide (Glc3Man9GlcNAc2-PP-Dol) where dolichol phosphate mannose synthase (DPMS) plays a central role...
June 14, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28616711/integrating-noe-and-rdc-using-sum-of-squares-relaxation-for-protein-structure-determination
#8
Y Khoo, A Singer, D Cowburn
We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints are too imprecise and sparse for accurate structure determination. Residual dipolar coupling (RDC) measurements provide additional geometric information on the angles between atom-pair directions and axes of the principal-axis-frame...
June 14, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28616083/outer-membrane-phospholipase-a-s-roles-in-helicobacter-pylori-acid-adaptation
#9
Hilde S Vollan, Tone Tannæs, Dominique A Caugant, Gert Vriend, Geir Bukholm
BACKGROUND: The pH of the human gastric mucosa varies around 2.5 so that only bacteria with strong acidic stress tolerance can colonize it. The ulcer causing Helicobacter pylori thrives in the gastric mucosa. We analyse the roles of the key outer membrane protein OMPLA in its roles in acid tolerance. RESULTS: The homology model of Helicobacter pylori outer membrane phospholipase A (OMPLA) reveals a twelve stranded β-barrel with a pore that allows molecules to pass with a diameter up to 4 Å...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28611792/structural-and-functional-insights-into-wrky3-and-wrky4-transcription-factors-to-unravel-the-wrky-dna-w-box-complex-interaction-in-tomato-solanum-lycopersicum-l-a-computational-approach
#10
Mohd Aamir, Vinay K Singh, Mukesh Meena, Ram S Upadhyay, Vijai K Gupta, Surendra Singh
The WRKY transcription factors (TFs), play crucial role in plant defense response against various abiotic and biotic stresses. The role of WRKY3 and WRKY4 genes in plant defense response against necrotrophic pathogens is well-reported. However, their functional annotation in tomato is largely unknown. In the present work, we have characterized the structural and functional attributes of the two identified tomato WRKY transcription factors, WRKY3 (SlWRKY3), and WRKY4 (SlWRKY4) using computational approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28610996/from-cheminformatics-to-structure-based-design-web-services-and-desktop-applications-based-on-the-naomi-library
#11
Stefan Bietz, Therese Inhester, Florian Lauck, Kai Sommer, Mathias M von Behren, Rainer Fährrolfes, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Matthias Hilbig, Karen T Schomburg, Andrea Volkamer, Matthias Rarey
Nowadays, computational approaches are an integral part of life science research. Problems related to interpretation of experimental results, data analysis, or visualization tasks highly benefit from the achievements of the digital era. Simulation methods facilitate predictions of physicochemical properties and can assist in understanding macromolecular phenomena. Here, we will give an overview of the methods developed in our group that aim at supporting researchers from all life science areas. Based on state-of-the-art approaches from structural bioinformatics and cheminformatics, we provide software covering a wide range of research questions...
June 10, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28609675/covalent-inhibitors-an-opportunity-for-rational-target-selectivity
#12
REVIEW
Roman Lagoutte, Remi Patouret, Nicolas Winssinger
There is a resurging interest in compounds that engage their target through covalent interactions. Cysteine's thiol is endowed with enhanced reactivity, making it the nucleophile of choice for covalent engagement with a ligand aligning an electrophilic trap with a cysteine residue in a target of interest. The paucity of cysteine in the proteome coupled to the fact that closely related proteins do not necessarily share a given cysteine residue enable a level of unprecedented rational target selectivity. The recent demonstration that a lysine's amine can also be engaged covalently with a mild electrophile extends the potential of covalent inhibitors...
June 10, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28606861/the-molecular-characterizations-of-cu-znsod-and-mnsod-and-its-responses-of-mrna-expression-and-enzyme-activity-to-aeromonas-hydrophila-or-lipopolysaccharide-challenge-in-qihe-crucian-carp-carassius-auratus
#13
Xianghui Kong, Dan Qiao, Xianliang Zhao, Li Wang, Jie Zhang, Dandan Liu, Hongxu Zhang
Superoxide dismutases (SODs), as the prime antioxidant enzymes, present the first line of defense against oxidative stress caused by excessive reactive oxygen species (ROS) in organism. In the study, two distinct members of SOD family were cloned and analyzed in Qihe crucian carp Carassius auratus (designated as CaCu/ZnSOD and CaMnSOD, respectively). The full-length cDNA of CaCu/ZnSOD is 759 bp, containing a 5' -untranslated region (UTR) of 39 bp, a ORF (including stop codon, TAG) of 465 bp and a 3'-UTR of 255 bp...
June 10, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28603666/in-silico-analysis-reveals-widespread-presence-of-three-gene-families-mapk-mapkk-and-mapkkk-of-the-mapk-cascade-from-crop-plants-of-solanaceae-in-comparison-to-the-distantly-related-syntenic-species-from-rubiaceae-coffee
#14
Hira Iftikhar, Nayab Naveed, Nasar Virk, Muhammad Faraz Bhatti, Fengming Song
Mitogen-activated protein kinases (MAPKs) are an important family of genes which play roles in vital plant processes, and they also help in coping against various kinds of environmental stresses including abiotic as well as biotic factors. The advancement of genomics calls for the annotation, identification, and detailed processing of the essential gene families in plants in order to provide insights into the importance of their central roles as well as for providing the basis for making their growth vigorous even under stressed conditions and, ultimately, to benefit from them by foreseeing the potential threats to their growth...
2017: PeerJ
https://www.readbyqxmd.com/read/28597165/proteomic-characterization-and-bio-informatic-analysis-of-differentially-expressed-e-coli-nissle-1917-proteins-with-response-to-cocoti-wine-stress
#15
Chandrasekhar Kathera, Esther Lebonah Dulla, Venkata Prasad Chinahadri, Thanu Sree Mallakuntla Ramesh, Sreedevi Basavaraju, Pramodakumari Jasti
The present study emphases the comparative proteomic analysis of Escherichia coli Nissle 1917 under cocoti palm wine stress and identified differentially expressed proteins. Protein samples were analyzed by 2-D, MALDI-TOF combined with MS access. In 2-D electrophoresis, eight differentially expressed proteins were identified: five up-regulated, two down-regulated and one newly expressed protein. Protein spots were digested with trypsin for MALDI-TOF-MS analysis; protein sequences were obtained from MASCOT search...
June 2017: 3 Biotech
https://www.readbyqxmd.com/read/28595570/plant-pectin-acetylesterase-structure-and-function-new-insights-from-bioinformatic-analysis
#16
Florian Philippe, Jérôme Pelloux, Catherine Rayon
BACKGROUND: Pectins are plant cell wall polysaccharides that can be acetylated on C2 and/or C3 of galacturonic acid residues. The degree of acetylation of pectin can be modulated by pectin acetylesterase (EC 3.1.1.6, PAE). The function and structure of plant PAEs remain poorly understood and the role of the fine-tuning of pectin acetylation on cell wall properties has not yet been elucidated. RESULTS: In the present study, a bioinformatic approach was used on 72 plant PAEs from 16 species among 611 plant PAEs available in plant genomic databases...
June 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28583067/pfasum-a-substitution-matrix-from-pfam-structural-alignments
#17
Frank Keul, Martin Hess, Michael Goesele, Kay Hamacher
BACKGROUND: Detecting homologous protein sequences and computing multiple sequence alignments (MSA) are fundamental tasks in molecular bioinformatics. These tasks usually require a substitution matrix for modeling evolutionary substitution events derived from a set of aligned sequences. Over the last years, the known sequence space increased drastically and several publications demonstrated that this can lead to significantly better performing matrices. Interestingly, matrices based on dated sequence datasets are still the de facto standard for both tasks even though their data basis may limit their capabilities...
June 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28582591/a-tool-for-integrating-genetic-and-mass-spectrometry-based-peptide-data-proteogenomics-viewer-pv-a-genome-browser-like-tool-which-includes-ms-data-visualization-and-peptide-identification-parameters
#18
REVIEW
José Eduardo Kroll, Vandeclécio Lira da Silva, Sandro José de Souza, Gustavo Antonio de Souza
In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts...
June 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28582575/the-rna-workbench-best-practices-for-rna-and-high-throughput-sequencing-bioinformatics-in-galaxy
#19
Björn A Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen C Lott, Youri Hoogstrate, Wolfgang R Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F Stadler, Rolf Backofen
RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds...
June 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28581735/covalent-capture-of-aligned-self-assembling-nanofibers
#20
I-Che Li, Jeffrey D Hartgerink
A great deal of effort has been invested in the design and characterization of systems which spontaneously assemble into nanofibers. These systems are interesting for their fundamental supramolecular chemistry and have also been shown to be promising materials, particularly for biomedical applications. Multidomain peptides are one such assembler, and in previous work we have demonstrated the reversibility of their assembly under mild and easily controlled conditions, along with their utility for time-controlled drug delivery, protein delivery, cell encapsulation, and cell delivery applications...
June 14, 2017: Journal of the American Chemical Society
keyword
keyword
80658
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"