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Rosetta protein

Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
Obdulia Rabal, Fernando Pastor, Helena Villanueva, Mario M Soldevilla, Sandra Hervas-Stubbs, Julen Oyarzabal
Complementing Systematic Evolution of Ligands by EXponential Enrichment (SELEX) technologies with in silico prediction of aptamer binders has attracted a lot of interest in the recent years. We propose a workflow involving 2D structure prediction, 3D RNA modeling using Rosetta and docking to the target protein with 3dRPC for: (i) prediction of the binding mode of our two previously reported potent (Kd < 50 nmol/l) murine TIM3 aptamers, and (ii) the prioritization of TIM3 aptamers that were enriched in the SELEX workflow...
October 18, 2016: Molecular Therapy. Nucleic Acids
Ji-Hua Yu, Yang-Yang Li, Mian Xiang, Jian-Quan Zhu, Xin-He Huang, Wan-Jun Wang, Rui Tan, Jia-Yu Zhou, Hai Liao
OBJECTIVES: To clone and characterize a novel bi-functional α-amylase/subtilisin inhibitor (LASI) from the rhizome of Ligusticum chuanxiong, a traditional Chinese medicine. RESULTS: The LASI showed strong homology with members of the Kunitz trypsin inhibitor family. Its putative amino acid sequence has a 40 % identity with that of the α-amylase/subtilisin inhibitor from rice. LASI gene without signal peptide was expressed in E. coli Rosetta. After purification, the recombinant LASI protein was inhibitory against not only α-amylase from porcine pancreas, Helicoverpa armigera, Spodoptera litura and Plutella xylostella, but also subtilisin A, but not against trypsin or chymotrypsin...
October 17, 2016: Biotechnology Letters
Leah D McGurn, Maryam Moazami-Goudarzi, Sean A White, Tannu Suwal, Beant Brar, Jason Q Tang, George S Espie, Matthew S Kimber
CcaA is a b-carbonic anhydrase that is a component of the carboxysomes of a subset of b-cyanobacteria. This protein, which has a characteristic C-terminal extension of unknown function, is recruited to the carboxysome via interactions with CcmM, which is itself a γ-carbonic anhydrase homolog with enzymatic activity in many, but not all cyanobacteria. We have determined the structure of CcaA from Synechocystis sp. PCC 6803 at 1.45 Å. In contrast to the dimer of dimers organization of most bacterial β-carbonic anhydrases, or the loose dimer-of-dimers-of-dimers organization found in the plant enzymes, CcaA shows a well-packed trimer-of-dimers organization...
October 11, 2016: Biochemical Journal
Jinchao Yu, Jessica Andreani, Françoise Ochsenbein, Raphaël Guerois
Computational protein-protein docking is of great importance for understanding protein interactions at the structural level. CAPRI (Critical Assessment of PRediction of Interactions) experiments provide the protein docking community with a unique opportunity to blindly test methods based on real-life cases and help accelerate methodology development. For CAPRI rounds 28-35, we used an automatic docking pipeline integrating the coarse-grained co-evolution-based potential InterEvScore. This score was developed to exploit the information contained in the multiple sequence alignments of binding partners and selectively recognize co-evolved interfaces...
October 4, 2016: Proteins
Caitlin A Kowalsky, Timothy A Whitehead
The comprehensive sequence determinants of cohesin to binding affinity towards type I dockerin from Clostridium thermocellum and Clostridium cellulolyticum was evaluated using deep mutational scanning coupled to yeast surface display. We measured the relative binding affinity to dockerin for 2,970 and 2,778 single point mutants of C.thermocellum and C. cellulolyticum, respectively, representing over 96% of all possible single point mutants. The interface ΔΔG for each variant was reconstructed from sequencing counts and compared with three independent experimental methods...
October 3, 2016: Proteins
Karolis Uziela, Nanjiang Shu, Björn Wallner, Arne Elofsson
Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function...
October 4, 2016: Scientific Reports
Kristoffer E Johansson, Nicolai Tidemand Johansen, Signe Christensen, Scott Horowitz, James C A Bardwell, Johan G Olsen, Martin Willemoës, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Hamelryck, Jakob R Winther
Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria...
October 23, 2016: Journal of Molecular Biology
Lichao Zhang, Zongwei Li, Tonglin Shi, Xiaoqin La, Hanqing Li, Zhuoyu Li
BACKGROUND: Targeted therapies for cancer, especially the malignant cancer, are always restricted by the deficiency of tumor-specific drug delivery methods. Subtilase cytotoxic is a virulent cytotoxin, and the subunit A (SubA) of it is able to destroy the structure of glucose-regulated protein 78 (GRP78) to induce cell apoptosis, and to be expected as anti-cancer drugs, however, the ubiquitous receptor of subunit B of Subtilase cytotoxic (SubB) restricts its application on cancer therapy...
2016: BMC Biotechnology
Hongxing He, Hengrui Fang, Mitchell D Miller, George N Phillips, Wu Pei Su
An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationship of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed...
September 1, 2016: Acta Crystallographica. Section A, Foundations and Advances
Tomasz Stenzel, Grzegorz Woźniakowski, Daria Pestka, Dariusz Choszcz, Bartłomiej Tykałowski, Marcin Śmiałek, Andrzej Koncicki
The aim of this study was to evaluate the serologic status of domestic pigeons not infected and asymptomatically infected with the pigeon circovirus (PiCV) with the use of an enzyme-linked assay based on PiCV recombinant capsid protein as a plate antigen. Recombinant PiCV capsid protein was produced by transforming E. coli BL21 (DE3) Rosetta colonies with expression plasmids.Blood samples and cloacal swabs were collected from 171 asymptomatic pigeons. The birds were divided into two groups (infected and not infected with PiCV) based on the results of Sybr Green real time PCR screening for the presence of PiCV genetic material...
August 30, 2016: Poultry Science
Brett M Kroncke, Amanda M Duran, Jeffrey L Mendenhall, Jens Meiler, Jeffrey D Blume, Charles R Sanders
There is a compelling and growing need to accurately predict the impact of amino acid mutations on protein stability for problems in personalized medicine and other applications. Here the ability of 10 computational tools to accurately predict mutation-induced perturbation of folding stability (ΔΔG) for membrane proteins of known structure was assessed. All methods for predicting ΔΔG values performed significantly worse when applied to membrane proteins than when applied to soluble proteins, yielding estimated concordance, Pearson, and Spearman correlation coefficients of <0...
September 13, 2016: Biochemistry
Christoph Hartlmüller, Christoph Göbl, Tobias Madl
An approach to the de novo structure prediction of proteins is described that relies on surface accessibility data from NMR paramagnetic relaxation enhancements by a soluble paramagnetic compound (sPRE). This method exploits the distance-to-surface information encoded in the sPRE data in the chemical shift-based CS-Rosetta de novo structure prediction framework to generate reliable structural models. For several proteins, it is demonstrated that surface accessibility data is an excellent measure of the correct protein fold in the early stages of the computational folding algorithm and significantly improves accuracy and convergence of the standard Rosetta structure prediction approach...
September 19, 2016: Angewandte Chemie
Agnieszka A Kaczor, Manuela Jörg, Ben Capuano
In order to apply structure-based drug design techniques to G protein-coupled receptor complexes, it is essential to model their 3D structure and to identify regions that are suitable for selective drug binding. For this purpose, we have developed and tested a multi-component protocol to model the inactive conformation of the dopamine D2 receptor dimer, suitable for interaction with homobivalent antagonists. Our approach was based on protein-protein docking, applying the Rosetta software to obtain populations of dimers as present in membranes with all the main possible interfaces...
September 2016: Journal of Molecular Modeling
Brian J Bender, Alberto Cisneros, Amanda M Duran, Jessica A Finn, Darwin Fu, Alyssa D Lokits, Benjamin K Mueller, Amandeep K Sangha, Marion F Sauer, Alexander M Sevy, Gregory Sliwoski, Jonathan H Sheehan, Frank DiMaio, Jens Meiler, Rocco Moretti
Previously, we published an article providing an overview of the Rosetta suite of biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, K. W., et al. (2010) Biochemistry 49, 2987-2998]. The overwhelming positive response to this publication we received motivates us to here share the next iteration of these tutorials that feature de novo folding, comparative modeling, loop construction, protein docking, small molecule docking, and protein design. This updated and expanded set of tutorials is needed, as since 2010 Rosetta has been fully redesigned into an object-oriented protein modeling program Rosetta3...
August 30, 2016: Biochemistry
Bin-Bin Pan, Feng Yang, Yansheng Ye, Qiong Wu, Conggang Li, Thomas Huber, Xun-Cheng Su
Determining the three-dimensional structure of a protein in living cells remains particularly challenging. We demonstrated that the integration of site-specific tagging proteins and GPS-Rosetta calculations provides a fast and effective way of determining the structures of proteins in living cells, and in principle the interactions and dynamics of protein-ligand complexes.
August 11, 2016: Chemical Communications: Chem Comm
Yan Qin, Deanne W Sammond, Esther Braselmann, Margaret C Carpenter, Amy E Palmer
Various fluorescent probes have been developed to reveal the biological functions of intracellular labile Zn(2+). Here, we present Green Zinc Probe (GZnP), a novel genetically encoded Zn(2+) sensor design based on a single fluorescent protein (single-FP). The GZnP sensor is generated by attaching two zinc fingers (ZF) of the transcription factor Zap1 (ZF1 and ZF2) to the two ends of a circularly permuted green fluorescent protein (cpGFP). Formation of ZF folds induces interaction between the two ZFs, which induces a change in the cpGFP conformation, leading to an increase in fluorescence...
October 21, 2016: ACS Chemical Biology
Sheng Wu, Weida Pan, Xianli Shi, Auwalu Yusuf Abdullahi, Zhen Wang, Xingang Yu, Biao Jiang, Kangxin Li, Chang Xu, Guoqing Li
To study subcellular localization of α18- and α12-giardin in Giardia lamblia trophozoites, the α18- and α12-giardin genes were amplified from G. lamblia assemblage A, respectively. The PCR products were cloned into the prokaryotic expression vector pET-28a(+), and the positive recombinant plasmids were transformed into E. coli Rosetta (DE3) strain for the expression, and expressed α18- and α12-giardin fusion protein were purified by Ni-Agarose resin, respectively. Mice were immunized with purified fusion proteins for preparation of polyclonal antibody, and then the subcellular localization of α18- and α12-giardin was determined by fluorescence immunoassay...
November 2016: Parasitology Research
Sonnhild Mittag, Tomas Valenta, Jörg Weiske, Laura Bloch, Susanne Klingel, Dietmar Gradl, Franziska Wetzel, Yuan Chen, Iver Petersen, Konrad Basler, Otmar Huber
Nitrilase1 was classified as a tumour suppressor in association with the fragile histidine-triad protein Fhit. However, knowledge about nitrilase1 and its tumour suppressor function is still limited. Whereas nitrilase1 and Fhit are discrete proteins in mammals, they are merged in Drosophila melanogaster and Caenorhabditis elegans. According to the Rosetta-Stone hypothesis, proteins encoded as fusion proteins in one organism and as separate proteins in another organism may act in the same signalling pathway...
2016: Cell Discovery
Jinyeong Kim, Seul I Kim, Eunsoo Hong, Yeonwoo Ryu
Heterologous proteins expressed in bacteria are used for numerous biotechnological applications. Escherichia coli is the most commonly used host for heterologous protein expression because of its many advantages. Researchers have been studying proteins from extremophiles heterologously expressed in E. coli because the proteins of extremophiles are strongly resistant to extreme conditions. In a previous study, a thermostable esterase Est-AF was isolated from Archaeoglobus fulgidus and expressed in E. coli...
November 2016: Protein Expression and Purification
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