keyword
MENU ▼
Read by QxMD icon Read
search

Rosetta protein

keyword
https://www.readbyqxmd.com/read/28318014/-solvent-hydrogen-bond-occlusion-a-new-model-of-polar-desolvation-for-biomolecular-energetics
#1
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...
March 20, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28302718/a-unique-choanoflagellate-enzyme-rhodopsin-with-cyclic-nucleotide-phosphodiesterase-activity
#2
Kazuho Yoshida, Satoshi P Tsunoda, Leonid S Brown, Hideki Kandori
Photoactivated adenylyl cyclase (PAC) and guanylyl cyclase rhodopsin (Rh-GC) increase the concentrations of intracellular cyclic nucleotides upon illumination, serving as promising second-generation tools in optogenetics. To broaden arsenal of such tools, it is desirable to have light-activatable enzymes which can decrease cyclic nucleotide concentrations in cells. Here, we report on an unusual microbial rhodopsin which 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...
March 16, 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
#3
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 E...
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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...
January 31, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28133815/comparison-of-nutritional-and-antinutritional-traits-among-different-species-lupinus-albus-l-lupinus-luteus-l-lupinus-angustifolius-l-and-varieties-of-lupin-seeds
#10
N Musco, M I Cutrignelli, S Calabrò, R Tudisco, F Infascelli, R Grazioli, V Lo Presti, F Gresta, B Chiofalo
In order to promote the use of lupin in pig nutrition, in this research the nutritional characteristics (i.e. dietary fibre, alkaloid and fatty acid profile) and the in vitro gas production of 12 lupin varieties grown in the Mediterranean basin and belonging to three lupin species (Lupinus albus, Lupinus angustifolius and Lupinus luteus) were assessed. Four varieties of L. albus (Asfer, Lublanc, Lutteur and Multitalia) were grown in South Campania. Three varieties of L. luteus (Dukat, Mister and Taper), three of L...
January 30, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28125104/modeling-and-docking-of-antibody-structures-with-rosetta
#11
Brian D Weitzner, Jeliazko R Jeliazkov, Sergey Lyskov, Nicholas Marze, Daisuke Kuroda, Rahel Frick, Jared Adolf-Bryfogle, Naireeta Biswas, Roland L Dunbrack, Jeffrey J Gray
We describe Rosetta-based computational protocols for predicting the 3D structure of an antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock). Antibody modeling leverages canonical loop conformations to graft large segments from experimentally determined structures, as well as offering (i) energetic calculations to minimize loops, (ii) docking methodology to refine the VL-VH relative orientation and (iii) de novo prediction of the elusive complementarity determining region (CDR) H3 loop...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28104891/protein-structure-determination-using-metagenome-sequence-data
#12
Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A Pavlopoulos, David E Kim, Hetunandan Kamisetty, Nikos C Kyrpides, David Baker
Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank...
January 20, 2017: Science
https://www.readbyqxmd.com/read/28096444/single-molecule-fret-rosetta-reveals-rna-structural-rearrangements-during-human-telomerase-catalysis
#13
Joseph W Parks, Kalli Kappel, Rhiju Das, Michael D Stone
Maintenance of telomeres by telomerase permits continuous proliferation of rapidly dividing cells, including the majority of human cancers. Despite its direct biomedical significance, the architecture of the human telomerase complex remains unknown. Generating homogeneous telomerase samples has presented a significant barrier to developing improved structural models. Here we pair single-molecule Förster resonance energy transfer (smFRET) measurements with Rosetta modeling to map the conformations of the essential telomerase RNA core domain within the active ribonucleoprotein...
February 2017: RNA
https://www.readbyqxmd.com/read/28096331/one-step-design-of-a-stable-variant-of-the-malaria-invasion-protein-rh5-for-use-as-a-vaccine-immunogen
#14
Ivan Campeotto, Adi Goldenzweig, Jack Davey, Lea Barfod, Jennifer M Marshall, Sarah E Silk, Katherine E Wright, Simon J Draper, Matthew K Higgins, Sarel J Fleishman
Many promising vaccine candidates from pathogenic viruses, bacteria, and parasites are unstable and cannot be produced cheaply for clinical use. For instance, Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) is essential for erythrocyte invasion, is highly conserved among field isolates, and elicits antibodies that neutralize in vitro and protect in an animal model, making it a leading malaria vaccine candidate. However, functional RH5 is only expressible in eukaryotic systems and exhibits moderate temperature tolerance, limiting its usefulness in hot and low-income countries where malaria prevails...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28089880/a-combined-approach-for-enhancing-the-stability-of-recombinant-cis-dihydrodiol-naphthalene-dehydrogenase-from-pseudomonas-putida-g7-allowed-for-the-structural-and-kinetic-characterization-of-the-enzyme
#15
Débora Maria Abrantes Costa, Mariana Amalia Figueiredo Costa, Samuel Leite Guimarães, Juliana Barbosa Coitinho, Stefanya Velásquez Gómez, Tiago Antônio da Silva Brandão, Ronaldo Alves Pinto Nagem
The second enzyme of the naphthalene degradation pathway in Pseudomonas putida G7 is NahB, a dehydrogenase that converts cis-1,2-dihydroxy-1,2-dihydronaphthalene to 1,2-dihydroxynaphthalene. We report the cloning, optimization of expression, purification, kinetic studies and preliminary structural characterization of the recombinant NahB. The nahB gene was cloned into a T7 expression vector and the enzyme was overexpressed in Escherichia coli Rosetta (DE3) as an N-terminal hexa-histidine-tagged protein (6xHis-NahB)...
January 9, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28066917/balancing-exploration-and-exploitation-in-population-based-sampling-improves-fragment-based-de-novo-protein-structure-prediction
#16
David Simoncini, Thomas Schiex, Kam Y J Zhang
Conformational search space exploration remains a major bottleneck for protein structure prediction methods. Population-based meta-heuristics typically enable the possibility to control the search dynamics and to tune the balance between local energy minimization and search space exploration. EdaFold is a fragment-based approach that can guide search by periodically updating the probability distribution over the fragment libraries used during model assembly. We implement the EdaFold algorithm as a Rosetta protocol and provide two different probability update policies: a cluster-based variation (EdaRosec ) and an energy-based one (EdaRoseen ) We analyze the search dynamics of our new Rosetta protocols and show that EdaRosec EdaRosec is able to provide predictions with lower Cα RMSD to the native structure than EdaRoseen and Rosetta AbInitio Relax protocol...
January 9, 2017: Proteins
https://www.readbyqxmd.com/read/28052191/engineering-a-thermostable-keto-acid-decarboxylase-using-directed-evolution-and-computationally-directed-protein-design
#17
Lemuel M J Soh, Wai Shun Mak, Paul P Lin, Luo Mi, Frederic Y-H Chen, Robert Damoiseaux, Justin B Siegel, James C Liao
Keto acid decarboxylase (Kdc) is a key enzyme in producing keto acid derived higher alcohols, like isobutanol. The most active Kdc's are found in mesophiles; the only reported Kdc activity in thermophiles is 2 orders of magnitude less active. Therefore, the thermostability of mesophilic Kdc limits isobutanol production temperature. Here, we report development of a thermostable 2-ketoisovalerate decarboxylase (Kivd) with 10.5-fold increased residual activity after 1h preincubation at 60 °C. Starting with mesophilic Lactococcus lactis Kivd, a library was generated using random mutagenesis and approximately 8,000 independent variants were screened...
January 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28045385/crystal-structure-of-human-chondroadherin-solving-a-difficult-molecular-replacement-problem-using-de-novo-models
#18
Sebastian Rämisch, Anna Pramhed, Viveka Tillgren, Anders Aspberg, Derek T Logan
Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1 integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28011777/expanding-the-toolkit-for-membrane-protein-modeling-in-rosetta
#19
Julia Koehler Leman, Benjamin K Mueller, Jeffrey J Gray
MOTIVATION: A range of membrane protein modeling tools has been developed in the past 5-10 years, yet few of these tools are integrated and make use of existing functionality for soluble proteins. To extend existing methods in the Rosetta biomolecular modeling suite for membrane proteins, we recently implemented RosettaMP, a general framework for membrane protein modeling. While RosettaMP facilitates implementation of new methods, addressing real-world biological problems also requires a set of accessory tools that are used to carry out standard modeling tasks...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28002624/flexpepdock-lessons-from-capri-peptide-protein-rounds-and-suggested-new-criteria-for-assessment-of-model-quality-and-utility
#20
Orly Marcu, Emma-Joy Dodson, Nawsad Alam, Michal Sperber, Dima Kozakov, Marc F Lensink, Ora Schueler-Furman
CAPRI rounds 28 and 29 included, for the first time, peptide-receptor targets of three different systems, reflecting increased appreciation of the importance of peptide-protein interactions. The CAPRI rounds allowed us to objectively assess the performance of Rosetta FlexPepDock, one of the first protocols to explicitly include peptide flexibility in docking, accounting for peptide conformational changes upon binding. We discuss here successes and challenges in modeling these targets: we obtain top-performing, high-resolution models of the peptide motif for cases with known binding sites but there is a need for better modeling of flanking regions, as well as better selection criteria, in particular for unknown binding sites...
December 21, 2016: Proteins
keyword
keyword
73327
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"