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Protein structure alignment

Christian Helbing, Robert Stößel, Dominik A Hering, Matthias Michael Lothar Arras, Jörg Bossert, Klaus D Jandt
Nanostructured surfaces have the potential to influence the assembly as well as the orientation of adsorbed proteins and may, thus, strongly influence the biomaterials performance. For the class of polymeric (bio)materials a reproducible and well characterized nanostructure is the ordered chain folded surface of a polyethylene single crystal (PE-SC). We tested the hypothesis that the trinodal-rod shaped protein human plasma fibrinogen (HPF) adsorbs on the (001) surface of PE-SCs along specific crystallographic directions...
October 24, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Allan M Showalter, Brian D Keppler, Xiao Liu, Jens Lichtenberg, Lonnie R Welch
BACKGROUND: Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). Chimeric and hybrid HRGPs, however, also exist. A bioinformatics approach is employed here to identify and classify AGPs, EXTs, PRPs, chimeric HRGPs, and hybrid HRGPs from the proteins predicted by the completed genome sequence of poplar (Populus trichocarpa)...
October 21, 2016: BMC Plant Biology
Lothar Esser, Fei Zhou, Yihui Zhou, Yumei Xiao, Wai-Kwan Tang, Chang-An Yu, Zhaohai Qin, Di Xia
The Complex III or cytochrome bc1 (cyt bc1) complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc1 is to couple the reaction of electron transfer (ET) from ubiquinol to cytochrome c to proton pumping across the membrane. Mechanistically, the ET reaction requires docking of its Rieske iron-sulfur protein (ISP) subunit to the quinol oxidation (QP) site of the complex. Formation of an H-bond between the ISP and the bound substrate was proposed to mediate the docking...
October 7, 2016: Journal of Biological Chemistry
Jeffrey Skolnick, Hongyi Zhou
Despite their different implementations, comparison of the best threading approaches to the prediction of evolutionary distant protein structures reveals that they tend to succeed or fail on the same protein targets. This is true despite the fact that the structural template library has good templates for all cases. Thus, a key question is why are certain protein structures threadable while others are not. Comparison with threading results on a set of artificial sequences selected for stability, further argues that the failure of threading is due to the nature of the protein structures themselves...
October 17, 2016: Journal of Physical Chemistry. B
Ashwani Jha, K M Flurchick, Marwan Bikdash, Dukka B Kc
Internally symmetric proteins are proteins that have a symmetrical structure in their monomeric single-chain form. Around 10-15% of the protein domains can be regarded as having some sort of internal symmetry. In this regard, we previously published SymD (symmetry detection), an algorithm that determines whether a given protein structure has internal symmetry by attempting to align the protein to its own copy after the copy is circularly permuted by all possible numbers of residues. SymD has proven to be a useful algorithm to detect symmetry...
2016: BioMed Research International
Xiaocui Chen, Jing Li, Zuowang Cheng, Yinghua Xu, Xia Wang, Xiaorui Li, Dongmei Xu, Carolyn M Kapron, Ju Liu
Cadmium (Cd) is a heavy metal and environmental pollutant. The kidney is the principal target organ of Cd exposure. Previously, we found that low concentration of Cd damages the integrity of the glomerular filtration barrier. However, little is known about the effects of Cd on renal mesangial cells, which provide structural support for the glomerular capillary loops and regulate intraglomerular blood flow. In this study, human renal mesangial cells (HRMCs) were cultured in the presence of serum and treated with 4 μM Cd...
October 7, 2016: International Journal of Environmental Research and Public Health
Shalini Sharma, Prasenjit Dhar, Aneesh Thakur, Vivek Sharma, Mandeep Sharma
AIM: The present study was conducted to detect the presence of canine parvovirus (CPV) among diarrheic dogs in Himachal Pradesh and to identify the most prevalent antigenic variant of CPV based on molecular typing and sequence analysis of VP2 gene. MATERIALS AND METHODS: A total of 102 fecal samples were collected from clinical cases of diarrhea or hemorrhagic gastroenteritis from CPV vaccinated or non-vaccinated dogs. Samples were tested using CPV-specific polymerase chain reaction (PCR) targeting VP2 gene, multiplex PCR for detection of CPV-2a and CPV-2b antigenic variants, and a PCR for the detection of CPV-2c...
September 2016: Veterinary World
Daniel Ian McSkimming, Shima Dastgheib, Timothy R Baffi, Dominic P Byrne, Samantha Ferries, Steven Thomas Scott, Alexandra C Newton, Claire E Eyers, Krzysztof J Kochut, Patrick A Eyers, Natarajan Kannan
Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats...
October 12, 2016: Molecular BioSystems
Thomas Gueudré, Carlo Baldassi, Marco Zamparo, Martin Weigt, Andrea Pagnani
Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are urgently needed. Such methods should connect multiple scales from evolutionary conserved interactions between families of homologous proteins, over the identification of specifically interacting proteins in the case of multiple paralogs inside a species, down to the prediction of residues being in physical contact across interaction interfaces...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Stefano Costanzi, Matthew Skorski, Alessandro Deplano, Brett Habermehl, Mary Mendoza, Keyun Wang, Michelle Biederman, Jessica Dawson, Jia Gao
With the present work we quantitatively studied the modellability of the inactive state of Class A G protein-coupled receptors (GPCRs). Specifically, we constructed models of one of the Class A GPCRs for which structures solved in the inactive state are available, namely the β2 AR, using as templates each of the other class members for which structures solved in the inactive state are also available. Our results showed a detectable linear correlation between model accuracy and model/template sequence identity...
October 4, 2016: Journal of Molecular Graphics & Modelling
Jonas Fredriksson, Viviane S de Paula, Ana Paula Valente, Fabio C L Almeida, Martin Billeter
We demonstrate for the first time a complete small protein characterization with the projection-decomposition approach, including full assignments as well as determination of the 3D fold. In TOCSY- and NOESY-type 4D experiments, pairing of signals from hydrogens and from their respective heavy atoms in decompositions represents a new problem. An approach, referred to as "DIADECOMP" (diagonal decomposition), is introduced to solve this problem; it consists of two separate decompositions of the input projections, differing in a 45° rotation of the spectral axes...
October 3, 2016: Journal of Magnetic Resonance
Pritha Ghosh, Oommen K Mathew, Ramanathan Sowdhamini
BACKGROUND: RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information...
October 7, 2016: BMC Bioinformatics
Gaurav Jerath, Prakash Kishore Hazam, Shashi Shekhar, Vibin Ramakrishnan
Polypeptide chain has an invariant main-chain and a variant side-chain sequence. How the side-chain sequence determines fold in terms of its chemical constitution has been scrutinized extensively and verified periodically. However, a focussed investigation on the directive effect of side-chain geometry may provide important insights supplementing existing algorithms in mapping the geometrical evolution of protein chains and its structural preferences. Geometrically, folding of protein structure may be envisaged as the evolution of its geometric variables: ϕ, and ψ dihedral angles of polypeptide main-chain directed by χ1, and χ2 of side chain...
2016: PloS One
Philip Prathipati, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi
The D3R 2015 grand drug design challenge provided a set of blinded challenges for evaluating the applicability of our protocols for pose and affinity prediction. In the present study, we report the application of two different strategies for the two D3R protein targets HSP90 and MAP4K4. HSP90 is a well-studied target system with numerous co-crystal structures and SAR data. Furthermore the D3R HSP90 test compounds showed high structural similarity to existing HSP90 inhibitors in BindingDB. Thus, we adopted an integrated docking and scoring approach involving a combination of both pharmacophoric and heavy atom similarity alignments, local minimization and quantitative structure activity relationships modeling, resulting in the reasonable prediction of pose [with the root mean square deviation (RMSD) values of 1...
October 6, 2016: Journal of Computer-aided Molecular Design
Huihua Yuan, Jinbao Qin, Jing Xie, Biyun Li, Zhepao Yu, Zhiyou Peng, Bingcheng Yi, Xiangxin Lou, Xinwu Lu, Yanzhong Zhang
This study was designed to assess the efficacy of hyaluronan (HA) functionalized well-aligned nanofibers of poly-l-lactic acid (PLLA) in modulating the phenotypic expression of vascular smooth muscle cells (vSMCs) for blood vessel regeneration. Highly aligned HA/PLLA nanofibers in core-shell structure were prepared using a novel stable jet electrospinning approach. Formation of a thin HA-coating layer atop each PLLA nanofiber surface endowed the uni-directionally oriented fibrous mats with increased anisotropic wettability and mechanical compliance...
September 15, 2016: Nanoscale
Ki Seong Eom, Jin Sung Cheong, Seung Jae Lee
Zinc finger proteins are among the most extensively applied metalloproteins in the field of biotechnology due to their unique structural and functional aspects as transcriptional and translational regulators. The classical zinc fingers are the largest family of zinc proteins and they provide critical roles in physiological systems from prokaryotes to eukaryotes. Two cysteine and two histidine residues (Cys₂His₂) coordinate to the zinc ion for the structural functions to generate a ββα fold, and this secondary structure supports specific interactions with their binding partners including DNA, RNA, lipids, proteins, and small molecules...
October 6, 2016: Journal of Microbiology and Biotechnology
Mohnad Abdalla, Ya Nan Dai, Chang Biao Chi, Wang Cheng, Dong Dong Cao, Kang Zhou, Wafa Ali, Yuxing Chen, Cong Zhao Zhou
Glutaredoxins (Grxs) constitute a superfamily of proteins that perform diverse biological functions. The Saccharomyces cerevisiae glutaredoxin Grx6 not only serves as a glutathione (GSH)-dependent oxidoreductase and as a GSH transferase, but also as an essential [2Fe-2S]-binding protein. Here, the dimeric structure of the C-terminal domain of Grx6 (holo Grx6C), bridged by one [2Fe-2S] cluster coordinated by the active-site Cys136 and two external GSH molecules, is reported. Structural comparison combined with multiple-sequence alignment demonstrated that holo Grx6C is similar to the [2Fe-2S] cluster-incorporated dithiol Grxs, which share a highly conserved [2Fe-2S] cluster-binding pattern and dimeric conformation that is distinct from the previously identified [2Fe-2S] cluster-ligated monothiol Grxs...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
Hu Cao, Yonggang Lu
With the rapid growth of known protein 3D structures in number, how to efficiently compare protein structures becomes an essential and challenging problem in computational structural biology. At present, many protein structure alignment methods have been developed. Among all these methods, flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying structure similarities between proteins, which have gone through conformational changes. It is also found that the methods based on aligned fragment pairs (AFPs) have a special advantage over other approaches in balancing global structure similarities and local structure similarities...
October 6, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
A V Raevsky, M Sharifi, D A Samofalova, P A Karpov, Y B Blume
Histone lysine acetylation is a reversible post-translational modification that does not involve changes in DNA sequences. Enzymes play an important role in developmental processes and their deregulation has been linked to the progression of diverse disorders. The HAT enzyme family fulfills an important role in various developmental processes mediated by the state of chromatin, and have been attributed to its deregulation. To understand acetylation mechanisms and their role in cell signaling, transcriptional regulation, and apoptosis, it is crucial to identify and analyze acetylation sites...
November 2016: Journal of Molecular Modeling
S Srivastava, S B Lal, D C Mishra, U B Angadi, K K Chaturvedi, S N Rai, A Rai
BACKGROUND: Protein structure comparison play important role in in silico functional prediction of a new protein. It is also used for understanding the evolutionary relationships among proteins. A variety of methods have been proposed in literature for comparing protein structures but they have their own limitations in terms of accuracy and complexity with respect to computational time and space. There is a need to improve the computational complexity in comparison/alignment of proteins through incorporation of important biological and structural properties in the existing techniques...
2016: Algorithms for Molecular Biology: AMB
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