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https://www.readbyqxmd.com/read/28549910/naturally-acquired-immune-responses-to-thrombospondin-related-adhesion-protein-trap-of-plasmodium-vivax-in-patients-from-areas-of-unstable-malaria-transmission
#1
Saeed Nazeri, Sedigheh Zakeri, Akram Abouie Mehrizi, Navid Dinparast Djadid
A key tool for the control, elimination, and eradication of Plasmodium vivax is the development of an effective vaccine. The thrombospondin-related adhesion protein (TRAP) is one of the major sporozoite antigens that plays an important role in the invasion of mosquito salivary glands and hepatocytes by sporozoites. The main goal of this study was to evaluate the naturally acquired antibodies to the P. vivax TRAP (PvTRAP) in patients from malaria-endemic areas of Iran (n=116), Afghanistan (n=50), and Pakistan (n=50)...
May 23, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28531185/thermal-stability-and-kinetic-constants-for-129-variants-of-a-family-1-glycoside-hydrolase-reveal-that-enzyme-activity-and-stability-can-be-separately-designed
#2
Dylan Alexander Carlin, Siena Hapig-Ward, Bill Wayne Chan, Natalie Damrau, Mary Riley, Ryan W Caster, Bowen Bethards, Justin B Siegel
Accurate modeling of enzyme activity and stability is an important goal of the protein engineering community. However, studies seeking to evaluate current progress are limited by small data sets of quantitative kinetic constants and thermal stability measurements. Here, we report quantitative measurements of soluble protein expression in E. coli, thermal stability, and Michaelis-Menten constants (kcat, KM, and kcat/KM) for 129 designed mutants of a glycoside hydrolase. Statistical analyses reveal that functional Tm is independent of kcat, KM, and kcat/KM in this system, illustrating that an individual mutation can modulate these functional parameters independently...
2017: PloS One
https://www.readbyqxmd.com/read/28513090/benchmarking-a-computational-design-method-for-the-incorporation-of-metal-ion-binding-sites-at-symmetric-protein-interfaces
#3
William A Hansen, Sagar D Khare
The design of novel metal-ion binding sites along symmetric axes in protein oligomers could provide new avenues for metalloenzyme design, construction of protein-based nanomaterials and novel ion transport systems. Here, we describe a computational design method, Symmetric Protein Recursive Ion-cofactor Sampling (SyPRIS), for locating constellations of backbone positions within oligomeric protein structures that are capable of supporting desired symmetrically coordinated metal ion(s) chelated by sidechains (chelant model)...
May 15, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28512576/applications-of-contact-predictions-to-structural-biology
#4
REVIEW
Felix Simkovic, Sergey Ovchinnikov, David Baker, Daniel J Rigden
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28501600/development-of-a-human-epidermal-growth-factor-derivative-with-egfr-blocking-and-depleted-biological-activities-a-comparative-in-vitro-study-using-egfr-positive-breast-cancer-cells
#5
Masomeh Mehrabi, Kamran Mansouri, Bijan Soleymani, Zohreh Hoseinkhani, Mohsen Shahlaie, Reza Khodarahmi
Epidermal growth factor (EGF) is a local growth factor that stimulates cell growth, proliferation, and differentiation by binding to its receptor EGFR. EGF and EGFR are involved in many aspects of the development of carcinomas. Because EGFR has been found to be over-expressed in many tumors of epithelial origin, it is a potential target for antitumor therapy. In this study we designed a mutated form of hEGF (mEGF) with a deletion of four amino acids residues (Gln(43), Tyr(44), Arg(45) and Asp(46)) in order to show importance of Leu spatial location for EGFR binding/activation...
May 10, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28481970/foldit-standalone-a-video-game-derived-protein-structure-manipulation-interface-using-rosetta
#6
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B Siegel, Firas Khatib, Seth Cooper
Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements...
May 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28470912/jumping-between-protein-conformers-using-normal-modes
#7
Swapnil Mahajan, Yves-Henri Sanejouand
The relationship between the normal modes of a protein and its functional conformational change has been studied for decades. However, using this relationship in a predictive context remains a challenge. In this work, we demonstrate that, starting from a given protein conformer, it is possible to generate in a single step model conformers that are less than 1 Å (Cα -RMSD) from the conformer which is the known endpoint of the conformational change, particularly when the conformational change is collective in nature...
May 3, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#8
Rebecca F Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram K Mulligan, Kalli Kappel, Jason W Labonte, Michael S Pacella, Richard Bonneau, Philip Bradley, Roland L Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J Gray
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15)...
May 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28412830/expression-and-immunogenicity-of-vp40-protein-of-zebov
#9
Yinbiao Wang, Xiao Liu, Ling Tao, Pengwei Xu, Xia Gao, Huijun Li, Zhongzhi Yang, Weidong Wu
BACKGROUND: EBOV outbreaks continue to threaten the world due to the absence of effective vaccines and therapeutics. Easy-to-use and rapid diagnostic tests for EBOV are highly desired for prevention and control of the EVD epidemic. METHODS: Escherichia coli expression system was used to express VP40 protein of Zaire Ebola virus (ZEBOV) as water-soluble protein upon optimization of temperature, time, and IPTG concentration. VP40 protein was purified through Ni-NTA affinity chromatography and applied to immunize rabbits for immunogenicity analysis...
April 2017: Archives of Iranian Medicine
https://www.readbyqxmd.com/read/28383276/predicting-the-initial-steps-of-salt-stable-cowpea-chlorotic-mottle-virus-capsid-assembly-with-atomistic-force-fields
#10
Zoltan Antal, Janos Szoverfi, Szilard N Fejer
Computational prediction of native protein-protein interfaces still remains a challenging task. In virus capsids, each protein unit is in contact with copies of itself through several interfaces. The relative strengths of the different contacts affect the dynamics of the assembly, especially if the process is hierarchical. We investigate the dimerization of the salt-stable cowpea chlorotic mottle virus (CCMV) capsid protein using a combination of different computational tools. The best predictions of dimer configurations provided by blind docking with ZDOCK are rescored using geometry optimization with the Amber and Rosetta force fields...
April 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28349025/optimization-of-the-expression-of-dt386-br2-fusion-protein-in-escherichia-coli-using-response-surface-methodology
#11
Fatemeh Shafiee, Mohammad Rabbani, Ali Jahanian-Najafabadi
BACKGROUND: The aim of this study was to determine the best condition for the production of DT386-BR2 fusion protein, an immunotoxin consisting of catalytic and translocation domains of diphtheria toxin fused to BR2, a cancer specific cell penetrating peptide, for targeted eradication of cancer cells, in terms of the host, cultivation condition, and culture medium. MATERIALS AND METHODS: Recombinant pET28a vector containing the codons optimized for the expression of the DT386-BR2 gene was transformed to different strains of Escherichia coli (E...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/28318014/-solvent-hydrogen-bond-occlusion-a-new-model-of-polar-desolvation-for-biomolecular-energetics
#12
Andrea Bazzoli, John Karanicolas
Water engages in two important types of interactions near biomolecules: it forms ordered "cages" around exposed hydrophobic regions, and it participates in hydrogen bonds with surface polar groups. Both types of interaction are critical to biomolecular structure and function, but explicitly including an appropriate number of solvent molecules makes many applications computationally intractable. A number of implicit solvent models have been developed to address this problem, many of which treat these two solvation effects separately...
June 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28302718/a-unique-choanoflagellate-enzyme-rhodopsin-exhibits-light-dependent-cyclic-nucleotide-phosphodiesterase-activity
#13
Kazuho Yoshida, Satoshi P Tsunoda, Leonid S Brown, Hideki Kandori
Photoactivated adenylyl cyclase (PAC) and guanylyl cyclase rhodopsin increase the concentrations of intracellular cyclic nucleotides upon illumination, serving as promising second-generation tools in optogenetics. To broaden the arsenal of such tools, it is desirable to have light-activatable enzymes that can decrease cyclic nucleotide concentrations in cells. Here, we report on an unusual microbial rhodopsin that may be able to meet the demand. It is found in the choanoflagellate Salpingoeca rosetta and contains a C-terminal cyclic nucleotide phosphodiesterase (PDE) domain...
May 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28300559/expression-purification-and-in-vitro-refolding-of-the-recombinant-truncated-saposin-like-protein-2-antigen-for-development-of-diagnosis-of-human-fascioliasis
#14
Abolfazl Mirzadeh, Zarrintaj Valadkhani, Asiyeh Yoosefy, Jalal Babaie, Majid Golkar, Ahmad Reza Esmaeili Rastaghi, Elham Kazemi-Rad, Keyhan Ashrafi
Early diagnosis of fascioliasis is critical in prevention of injury to the liver and bile ducts. Saposin-like protein (FhSAP-2) is probably the most ideal antigen of Fasciola hepatica for development of ELISA kits. SAP-2 has a conserved tertiary structure containing three disulfide bonds and conformational epitopes. Therefore, antigenicity of SAP-2 is greatly depends on disulfide bond formation and proper folding. We produced the recombinant truncated SAP-2 (rtSAP-2) in the SHuffle(®) T7 and Rosetta strain of Escherichia coli, in soluble and insoluble forms, respectively and purified by immobilized metal affinity chromatography (IMAC)...
March 11, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28236237/modeling-peptide-protein-structure-and-binding-using-monte-carlo-sampling-approaches-rosetta-flexpepdock-and-flexpepbind
#15
Nawsad Alam, Ora Schueler-Furman
Many signaling and regulatory processes involve peptide-mediated protein interactions, i.e., the binding of a short stretch in one protein to a domain in its partner. Computational tools that generate accurate models of peptide-receptor structures and binding improve characterization and manipulation of known interactions, help to discover yet unknown peptide-protein interactions and networks, and bring into reach the design of peptide-based drugs for targeting specific systems of medical interest.Here, we present a concise overview of the Rosetta FlexPepDock protocol and its derivatives that we have developed for the structure-based characterization of peptide-protein binding...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28219343/computing-structure-based-lipid-accessibility-of-membrane-proteins-with-mp_lipid_acc-in-rosettamp
#16
Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
BACKGROUND: Membrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane proteins, lipid accessibility is an essential property. Although programs are available for sequence-based prediction of lipid accessibility and structure-based identification of solvent-accessible surface area, the latter does not distinguish between water accessible and lipid accessible residues in membrane proteins...
February 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28210460/cloning-and-expression-of-clostridium-perfringens-type-d-vaccine-strain-epsilon-toxin-gene-in-e-coli-as-a-recombinant-vaccine-candidate
#17
Parastoo Aziminia, Reza Pilehchian-Langroudi, Kasra Esmaeilnia
BACKGROUND AND OBJECTIVES: Clostridium perfringens, a Gram-positive obligate anaerobic bacterium, is able to form resistant spores which are widely distributed in the environment. C. perfringens is subdivided into five types A to E based on its four major alpha, beta, epsilon and iota toxins. The aim of the present study was cloning and expression of C. perfringens type D vaccine strain epsilon toxin gene. MATERIALS AND METHODS: Genomic DNA was extracted and the epsilon toxin gene was amplified using Pfu DNA polymerase...
August 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/28202377/characterization-of-a-new-fungal-immunomodulatory-protein-fip-dsq2-from-dichomitus-squalens
#18
Shuying Li, Zhonghao Jiang, Lichao Sun, Xin Liu, Ying Huang, Fengzhong Wang, Fengjiao Xin
FIP-dsq2, a new immunomodulatory protein, was identified in Basidiomycota Dichomitus squalens by gene mining. FIP-dsq2 contained 111 amino acids with a molecular weight of 12.51kDa. FIP-dsq2 had a homology range of 51-65% to the reported FIPs. The predicted 3-dimensional model had more similar identical folding patterns in LZ-8 than for FIP-fve. Evolutionary analysis indicated substantial phylogenetic differences were existed with the other FIPs. Overexpression of a 14.07kDa soluble recombinant FIP-dsq2 (rFIP-dsq2) was achieved in Rosetta (pGEX-6P-1) and the purified recombinant protein was homodimer verified by gel filtration chromatography analysis...
March 20, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28160322/atlas-a-database-linking-binding-affinities-with-structures-for-wild-type-and-mutant-tcr-pmhc-complexes
#19
Tyler Borrman, Jennifer Cimons, Michael Cosiano, Michael Purcaro, Brian G Pierce, Brian M Baker, Zhiping Weng
The ATLAS (Altered TCR Ligand Affinities and Structures) database (https://zlab.umassmed.edu/atlas/web/) is a manually curated repository containing the binding affinities for wild-type and mutant T cell receptors (TCRs) and their antigens, peptides presented by the major histocompatibility complex (pMHC). The database links experimentally measured binding affinities with the corresponding three dimensional (3D) structures for TCR-pMHC complexes. The user can browse and search affinities, structures, and experimental details for TCRs, peptides, and MHCs of interest...
February 3, 2017: Proteins
https://www.readbyqxmd.com/read/28142198/incorporating-an-allosteric-regulatory-site-in-an-antibody-through-backbone-design
#20
Olga Khersonsky, Sarel J Fleishman
Allosteric regulation underlies living cells' ability to sense changes in nutrient and signaling-molecule concentrations, but the ability to computationally design allosteric regulation into non-allosteric proteins has been elusive. Allosteric-site design is complicated by the requirement to encode the relative stabilities of active and inactive conformations of the same protein in the presence and absence of both ligand and effector. To address this challenge, we used Rosetta to design the backbone of the flexible heavy-chain complementarity-determining region 3 (HCDR3), and used geometric matching and sequence optimization to place a Zn(2+) -coordination site in a fluorescein-binding antibody...
April 2017: Protein Science: a Publication of the Protein Society
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