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Protein structure alignment

Sònia Font Tellado, Silvia Chiera, Walter Bonani, Patrina S P Poh, Claudio Migliaresi, Antonella Motta, Elizabeth R Balmayor, Martijn van Griensven
The tendon/ligament-to-bone transition (enthesis) is a highly specialized interface tissue with structural gradients of extracellular matrix composition, collagen molecule alignment and mineralization. These structural features are essential for enthesis function, but are often not regenerated after injury. Tissue engineering is a promising strategy for enthesis repair. Engineering of complex tissue interfaces such as the enthesis is likely to require a combination of biophysical, biological and chemical cues to achieve functional tissue regeneration...
March 14, 2018: Acta Biomaterialia
Kiwoung Yang, Ujjal Kumar Nath, Manosh Kumar Biswas, Md Abdul Kayum, Go-Eun Yi, Jonghoon Lee, Tae-Jin Yang, Ill-Sup Nou
Plant mitochondrial genomes (mtDNAs) vary in sequence structure. We assembled the Brassica oleracea var. capitata mtDNA using a mean coverage depth of 25X whole genome sequencing (WGS) and confirmed the presence of eight contigs/fragments by BLASTZ using the previously reported KJ820683 and AP012988 mtDNA as reference. Assembly of the mtDNA sequence reads resulted in a circular structure of 219,975 bp. Our assembled mtDNA, NCBI acc. no. KU831325, contained 34 protein-coding genes, 3 rRNA genes, and 19 tRNA genes with similarity to the KJ820683 and AP012988 reference mtDNA...
2018: PloS One
María E Errasti, Claudia L Natalucci, Néstor O Caffini, Alejandra E Rotelli, Adriana Brullo, Bruno Maras, Sebastián A Trejo, Laura M I López
The primary structure of macrodontain I, a peptidase from Pseudananas macrodontes fruits, was determined using Edman's degradation. The enzyme is a non-glycosylated peptidase composed by 213 amino acids with a calculated molecular weight of 23,486.18 Da, pI value 6.99, and a molar extinction coefficient at 280 nm of 61,685 M-1  cm-1 . The alignment of the sequence of macrodontain I with those cysteine peptidases from species belonging to the family Bromeliaceae showed the highest identity degree (87.74%) against fruit bromelain...
March 15, 2018: Applied Biochemistry and Biotechnology
Zeinab Jahed, Darya Fadavi, Uyen T Vu, Ehsaneddin Asgari, G W Gant Luxton, Mohammad R K Mofrad
The LINC complex is found in a wide variety of organisms and is formed by the transluminal interaction between outer- and inner-nuclear-membrane KASH and SUN proteins, respectively. Most extensively studied are SUN1 and SUN2 proteins, which are widely expressed in mammals. Although SUN1 and SUN2 play functionally redundant roles in several cellular processes, more recent studies have revealed diverse and distinct functions for SUN1. While several recent in vitro structural studies have revealed the molecular details of various fragments of SUN2, no such structural information is available for SUN1...
March 13, 2018: Biophysical Journal
Gregory A Babbitt, Jamie S Mortensen, Erin E Coppola, Lily E Adams, Justin K Liao
Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures...
March 13, 2018: Biophysical Journal
Yan Liu, Xiaoyu Guan, Shengnan Liu, Meng Yang, Junhui Ren, Meng Guo, Zhihui Huang, Yaowei Zhang
Chinese cabbage ( Brassica rapa L. ssp . pekinensis ) is a widely cultivated and economically important vegetable crop with typical leaf curvature. The TCP (Teosinte branched1, Cycloidea, Proliferating cell factor) family proteins are plant-specific transcription factors (TFs) and play important roles in many plant biological processes, especially in the regulation of leaf curvature. In this study, 39 genes encoding TCP TFs are detected on the whole genome of B. rapa. Based on the phylogenetic analysis of TCPs between Arabidopsis thaliana and Brassica rapa , TCP genes of Chinese cabbage are named from BrTCP1a to BrTCP24b ...
March 14, 2018: International Journal of Molecular Sciences
Chengxin Zhang, Wei Zheng, Peter L Freddolino, Yang Zhang
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO, to deduce Gene Ontology attributes of proteins by combining sequence homology-based annotation with low-resolution structure prediction and comparison, and partner's-homology based protein-protein network mapping. The pipeline was tested on a large-scale set of 1000 non-redundant proteins from the CAFA3 experiment...
March 10, 2018: Journal of Molecular Biology
Daniel J Rigden, Jens M H Thomas, Felix Simkovic, Adam Simpkin, Martyn D Winn, Olga Mayans, Ronan M Keegan
Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20-40% of the overall structure for example, can succeed as search models where they can be isolated...
March 1, 2018: Acta Crystallographica. Section D, Structural Biology
Angelina D Schoenenberger, Jasper Foolen, Pascal Moor, Unai Silvan, Jess G Snedeker
Healthy tendon tissue features a highly aligned extracellular matrix that becomes disorganized with disease. Recent evidence suggests that inflammation coexists with early degenerative changes in tendon, and that crosstalk between immune-cells and tendon fibroblasts (TFs) can contribute to poor tissue healing. We hypothesized that a disorganized tissue architecture may predispose tendon cells to degenerative extracellular matrix remodeling pathways, particularly within a pro-inflammatory niche. This hypothesis was tested by analyzing human TFs cultured on electrospun polycaprolactone (PCL) mats with either highly aligned or randomly oriented fiber structures...
March 9, 2018: Acta Biomaterialia
Menuka Pallebage-Gamarallage, Sean Foxley, Ricarda A L Menke, Istvan N Huszar, Mark Jenkinson, Benjamin C Tendler, Chaoyue Wang, Saad Jbabdi, Martin R Turner, Karla L Miller, Olaf Ansorge
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a clinically and histopathologically heterogeneous neurodegenerative disorder, in which therapy is hindered by the rapid progression of disease and lack of biomarkers. Magnetic resonance imaging (MRI) has demonstrated its potential for detecting the pathological signature and tracking disease progression in ALS. However, the microstructural and molecular pathological substrate is poorly understood and generally defined histologically...
March 13, 2018: BMC Neuroscience
Sergey Melnikov, Kasidet Manakongtreecheep, Dieter Söll
Ribosomal proteins are indispensable components of a living cell, and yet their structures are remarkably diverse in different species. Here we use manually curated structural alignments to provide a comprehensive catalog of structural variations in homologous ribosomal proteins from bacteria, archaea, eukaryotes and eukaryotic organelles. By resolving numerous ambiguities and errors of automated structural and sequence alignments, we uncover a whole new class of structural variations, which reside within seemingly conserved segments of ribosomal proteins...
February 24, 2018: Molecular Biology and Evolution
Sajad Abdollahi, Iraj Rasooli, Seyed Latif Mousavi Gargari
Acinetobacter baumannii is an opportunistic multidrug resistant pathogen. TonB-dependent copper receptor is an outer membrane protein and has a role in binding of A. baumannii to host cell via attachment to fibronectin. Moreover, it is highly expressed in biofilm community. In this study the properties of copper receptor were analyzed in silico and its vaccine potential was investigated. TonB-dependent copper and iron receptor domains plus one plug domain at N-terminal were determined by domain analysis. Topology modeling showed 22 β-strands, 11 loops and 10 periplasmic turns...
March 7, 2018: Microbial Pathogenesis
Rajiv Gandhi Govindaraj, Michal Brylinski
BACKGROUND: Detecting similar ligand-binding sites in globally unrelated proteins has a wide range of applications in modern drug discovery, including drug repurposing, the prediction of side effects, and drug-target interactions. Although a number of techniques to compare binding pockets have been developed, this problem still poses significant challenges. RESULTS: We evaluate the performance of three algorithms to calculate similarities between ligand-binding sites, APoc, SiteEngine, and G-LoSA...
March 9, 2018: BMC Bioinformatics
Veronica J Larsson, Mohammed Hakim Jafferali, Balaje Vijayaraghavan, Ricardo A Figueroa, Einar Hallberg
We have investigated a possible role of the inner nuclear membrane protein, Samp1, in the mitotic machinery. Live cell imaging showed that Samp1aYFP distributed as filamentous structures in the mitotic spindle, partially co-localising with ß-tubulin. Samp1 depletion resulted in an increased frequency of cells with signs of chromosomal mis-segregation and prolonged metaphase, indicating problems with spindle assembly and/or chromosomal alignment. Consistently, mitotic spindles in Samp1 depleted cells contained significantly lower levels of ß-tubulin and γ-tubulin, phenotypes which were rescued by overexpression of Samp1aYFP...
March 7, 2018: Journal of Cell Science
T S Tikhomirova, R S Ievlev, M Yu Suvorina, L G Bobyleva, I M Vikhlyantsev, A K Surin, O V Galzitskaya
The scientific interest to the structural and functional properties of actin is determined by its abundance in cells. Being an important component of the cytoskeleton, actin is involved in many protein-protein interactions. Using crystal structures and molecular models, we have mapped the amino acid residues that are involved in these interactions and form the ATP-binding site of the actin monomer. Moreover, using mass spectrometry and high-performance liquid chromatography methods, we have discovered the regions of the amino acid sequence of actin that form the core of the actin fibril...
January 2018: Molekuliarnaia Biologiia
A M Kargatov, A V Efimov
Possible combinations of βαβ-units and Π-like modules in proteins in both right- and left-handed forms have been analyzed in detail. The correlation between the mutual arrangement of the structural elements in the polypeptide chain and their handedness has been shown. In the βαβП combinations, which is encountered most frequently in proteins, the П-module follows the βαβ unit along the chain and both elements are right-handed. In the Пβαβ combinations, where the П-module is located at the N end and the βαβ-unit follows it, the former is left-handed and the latter is right-handed...
January 2018: Molekuliarnaia Biologiia
Armen Abnousi, Shira L Broschat, Ananth Kalyanaraman
BACKGROUND: Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput sequencing technologies, new protein sequences are becoming available at an extraordinary rate. The rapid growth rate has impeded deployment of existing protein clustering/annotation tools which depend largely on pairwise sequence alignment. RESULTS: In this paper, we propose an alignment-free clustering approach, coreClust, for annotating protein sequences using detected conserved regions...
March 5, 2018: BMC Bioinformatics
Alan J Ryan, Cathal J Kearney, Nian Shen, Umar Khan, Adam G Kelly, Christopher Probst, Eva Brauchle, Sonia Biccai, Carolina D Garciarena, Victor Vega-Mayoral, Peter Loskill, Steve W Kerrigan, Daniel J Kelly, Katja Schenke-Layland, Jonathan N Coleman, Fergal J O'Brien
Electroconductive substrates are emerging as promising functional materials for biomedical applications. Here, the development of biohybrids of collagen and pristine graphene that effectively harness both the biofunctionality of the protein component and the increased stiffness and enhanced electrical conductivity (matching native cardiac tissue) obtainable with pristine graphene is reported. As well as improving substrate physical properties, the addition of pristine graphene also enhances human cardiac fibroblast growth while simultaneously inhibiting bacterial attachment (Staphylococcus aureus)...
March 5, 2018: Advanced Materials
Ye Li, Lei Chen, Jun Zhou, Xiurong Su, Taiwu Li
The gelsolin family proteins are best known for involvement in cytoskeletal rearrangement by controlling actin organization during a variety of cellular processes. Previously, a 1962 bp cDNA encoding a 41.7 kDa protein with three gelsolin-like domains (G domains) from Dendrorhynchus zhejiangensis was identified and named as DzGSN. In this study, the sequence and function of a novel member of the gelsolin family proteins from D. zhejiangensis have been analyzed. Sequence alignment indicates that DzGSN is highly homologous to human gelsolin (35% identity) and human CapG (36% identity)...
March 2, 2018: Protein Journal
Weiping Lin, Ao Liu, Caihong Weng, Hui Li, Shiwei Sun, Aihuan Song, Hu Zhu
Phenylalanine ammonia-lyase (PAL) gene plays an important role in the synthesis of flavones, lignin, and other bioactive compounds in living organisms. Inonotus baumii, the only known flavone-producing filamentous fungus, is of great importance in the investigation of flavone metabolic pathways. To study the function of PAL enzyme in I. baumii flavone synthesis, a full-length cDNA of pal gene was cloned from I. baumii using DOP-PCR and RACE-PCR. The 2502-bp PAL coding region encodes an 833 amino acid protein with an approximate MW of 88...
May 2018: Enzyme and Microbial Technology
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