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David baker rosetta

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https://www.readbyqxmd.com/read/27766851/simultaneous-optimization-of-biomolecular-energy-function-on-features-from-small-molecules-and-macromolecules
#1
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
https://www.readbyqxmd.com/read/26857542/structure-prediction-using-sparse-simulated-noe-restraints-with-rosetta-in-casp11
#2
Sergey Ovchinnikov, Hahnbeom Park, David E Kim, Yuan Liu, Ray Yu-Ruei Wang, David Baker
In CASP11 we generated protein structure models using simulated ambiguous and unambiguous nuclear Overhauser effect (NOE) restraints with a two stage protocol. Low resolution models were generated guided by the unambiguous restraints using continuous chain folding for alpha and alpha-beta proteins, and iterative annealing for all beta proteins to take advantage of the strand pairing information implicit in the restraints. The Rosetta fragment/model hybridization protocol was then used to recombine and regularize these models, and refine them in the Rosetta full atom energy function guided by both the unambiguous and the ambiguous restraints...
September 2016: Proteins
https://www.readbyqxmd.com/read/26374198/engineering-of-kuma030-a-gliadin-peptidase-that-rapidly-degrades-immunogenic-gliadin-peptides-in-gastric-conditions
#3
Clancey Wolf, Justin B Siegel, Christine Tinberg, Alessandra Camarca, Carmen Gianfrani, Shirley Paski, Rongjin Guan, Gaetano Montelione, David Baker, Ingrid S Pultz
Celiac disease is characterized by intestinal inflammation triggered by gliadin, a component of dietary gluten. Oral administration of proteases that can rapidly degrade gliadin in the gastric compartment has been proposed as a treatment for celiac disease; however, no protease has been shown to specifically reduce the immunogenic gliadin content, in gastric conditions, to below the threshold shown to be toxic for celiac patients. Here, we used the Rosetta Molecular Modeling Suite to redesign the active site of the acid-active gliadin endopeptidase KumaMax...
October 14, 2015: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/26335199/large-scale-determination-of-previously-unsolved-protein-structures-using-evolutionary-information
#4
Sergey Ovchinnikov, Lisa Kinch, Hahnbeom Park, Yuxing Liao, Jimin Pei, David E Kim, Hetunandan Kamisetty, Nick V Grishin, David Baker
The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available...
2015: ELife
https://www.readbyqxmd.com/read/26226626/improving-the-catalytic-performance-of-an-artificial-metalloenzyme-by-computational-design
#5
Tillmann Heinisch, Michela Pellizzoni, Marc Dürrenberger, Christine E Tinberg, Valentin Köhler, Juliane Klehr, Daniel Häussinger, David Baker, Thomas R Ward
Artifical metalloenzymes combine the reactivity of small molecule catalysts with the selectivity of enzymes, and new methods are required to tune the catalytic properties of these systems for an application of interest. Structure-based computational design could help to identify amino acid mutations leading to improved catalytic activity and enantioselectivity. Here we describe the application of Rosetta Design for the genetic optimization of an artificial transfer hydrogenase (ATHase hereafter), [(η(5)-Cp*)Ir(pico)Cl] ⊂ WT hCA II (Cp* = Me5C5(-)), for the asymmetric reduction of a cyclic imine, the precursor of salsolsidine...
August 19, 2015: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/26205421/casp11-refinement-experiments-with-rosetta
#6
Hahnbeom Park, Frank DiMaio, David Baker
We report new Rosetta-based approaches to tackling the major issues that confound protein structure refinement, and the testing of these approaches in the CASP11 experiment. Automated refinement protocols were developed that integrate a range of sampling methods using parallel computation and multiobjective optimization. In CASP11, we used a more aggressive large-scale structure rebuilding approach for poor starting models, and a less aggressive local rebuilding plus core refinement approach for starting models likely to be closer to the native structure...
September 2016: Proteins
https://www.readbyqxmd.com/read/25971965/computation-and-functional-studies-provide-a-model-for-the-structure-of-the-zinc-transporter-hzip4
#7
Sagar Antala, Sergey Ovchinnikov, Hetunandan Kamisetty, David Baker, Robert E Dempski
Members of the Zrt and Irt protein (ZIP) family are a central participant in transition metal homeostasis as they function to increase the cytosolic concentration of zinc and/or iron. However, the lack of a crystal structure hinders elucidation of the molecular mechanism of ZIP proteins. Here, we employed GREMLIN, a co-evolution-based contact prediction approach in conjunction with the Rosetta structure prediction program to construct a structural model of the human (h) ZIP4 transporter. The predicted contact data are best fit by modeling hZIP4 as a dimer...
July 17, 2015: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/25866491/combined-covalent-electrostatic-model-of-hydrogen-bonding-improves-structure-prediction-with-rosetta
#8
Matthew J O'Meara, Andrew Leaver-Fay, Michael D Tyka, Amelie Stein, Kevin Houlihan, Frank DiMaio, Philip Bradley, Tanja Kortemme, David Baker, Jack Snoeyink, Brian Kuhlman
Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in character and exhibit strong orientation preferences; at longer ranges the orientation preferences are lost, but significant electrostatic interactions between charged and partially charged atoms remain. To simultaneously model these two types of behavior, we refined an orientation dependent model of hydrogen bonds [Kortemme et al. J. Mol. Biol. 2003, 326, 1239] used by the molecular modeling program Rosetta and then combined it with a distance-dependent Coulomb model of electrostatics...
February 10, 2015: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/25707030/atomic-accuracy-models-from-4-5-%C3%A3-cryo-electron-microscopy-data-with-density-guided-iterative-local-refinement
#9
Frank DiMaio, Yifan Song, Xueming Li, Matthias J Brunner, Chunfu Xu, Vincent Conticello, Edward Egelman, Thomas C Marlovits, Yifan Cheng, David Baker
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method...
April 2015: Nature Methods
https://www.readbyqxmd.com/read/25700516/transition-states-trapping-a-transition-state-in-a-computationally-designed-protein-bottle
#10
Aaron D Pearson, Jeremy H Mills, Yifan Song, Fariborz Nasertorabi, Gye Won Han, David Baker, Raymond C Stevens, Peter G Schultz
The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl...
February 20, 2015: Science
https://www.readbyqxmd.com/read/25587134/the-nmr-rosetta-capsid-model-of-m13-bacteriophage-reveals-a-quadrupled-hydrophobic-packing-epitope
#11
Omry Morag, Nikolaos G Sgourakis, David Baker, Amir Goldbourt
Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16...
January 27, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/25451037/a-general-computational-approach-for-repeat-protein-design
#12
Fabio Parmeggiani, Po-Ssu Huang, Sergey Vorobiev, Rong Xiao, Keunwan Park, Silvia Caprari, Min Su, Jayaraman Seetharaman, Lei Mao, Haleema Janjua, Gaetano T Montelione, John Hunt, David Baker
Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability...
January 30, 2015: Journal of Molecular Biology
https://www.readbyqxmd.com/read/25388768/a-hybrid-nmr-saxs-based-approach-for-discriminating-oligomeric-protein-interfaces-using-rosetta
#13
Paolo Rossi, Lei Shi, Gaohua Liu, Christopher M Barbieri, Hsiau-Wei Lee, Thomas D Grant, Joseph R Luft, Rong Xiao, Thomas B Acton, Edward H Snell, Gaetano T Montelione, David Baker, Oliver F Lange, Nikolaos G Sgourakis
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology-based methods, protein-protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet-V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1...
February 2015: Proteins
https://www.readbyqxmd.com/read/25313043/computational-design-of-a-red-fluorophore-ligase-for-site-specific-protein-labeling-in-living-cells
#14
Daniel S Liu, Lucas G Nivón, Florian Richter, Peter J Goldman, Thomas J Deerinck, Jennifer Z Yao, Douglas Richardson, William S Phipps, Anne Z Ye, Mark H Ellisman, Catherine L Drennan, David Baker, Alice Y Ting
Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons...
October 28, 2014: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/25264107/high-resolution-structure-of-the-shigella-type-iii-secretion-needle-by-solid-state-nmr-and-cryo-electron-microscopy
#15
Jean-Philippe Demers, Birgit Habenstein, Antoine Loquet, Suresh Kumar Vasa, Karin Giller, Stefan Becker, David Baker, Adam Lange, Nikolaos G Sgourakis
We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information...
September 29, 2014: Nature Communications
https://www.readbyqxmd.com/read/24646222/centenary-award-and-sir-frederick-gowland-hopkins-memorial-lecture-protein-folding-structure-prediction-and-design
#16
David Baker
I describe how experimental studies of protein folding have led to advances in protein structure prediction and protein design. I describe the finding that protein sequences are not optimized for rapid folding, the contact order-protein folding rate correlation, the incorporation of experimental insights into protein folding into the Rosetta protein structure production methodology and the use of this methodology to determine structures from sparse experimental data. I then describe the inverse problem (protein design) and give an overview of recent work on designing proteins with new structures and functions...
April 2014: Biochemical Society Transactions
https://www.readbyqxmd.com/read/24510272/redesigning-the-specificity-of-protein-dna-interactions-with-rosetta
#17
Summer Thyme, David Baker
Building protein tools that can selectively bind or cleave specific DNA sequences requires efficient technologies for modifying protein-DNA interactions. Computational design is one method for accomplishing this goal. In this chapter, we present the current state of protein-DNA interface design with the Rosetta macromolecular modeling program. The LAGLIDADG endonuclease family of DNA-cleaving enzymes, under study as potential gene therapy reagents, has been the main testing ground for these in silico protocols...
2014: Methods in Molecular Biology
https://www.readbyqxmd.com/read/24392845/protein-nmr-structures-refined-with-rosetta-have-higher-accuracy-relative-to-corresponding-x-ray-crystal-structures
#18
Binchen Mao, Roberto Tejero, David Baker, Gaetano T Montelione
We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5-22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures...
February 5, 2014: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/24076763/improved-low-resolution-crystallographic-refinement-with-phenix-and-rosetta
#19
Frank DiMaio, Nathaniel Echols, Jeffrey J Headd, Thomas C Terwilliger, Paul D Adams, David Baker
Refinement of macromolecular structures against low-resolution crystallographic data is limited by the ability of current methods to converge on a structure with realistic geometry. We developed a low-resolution crystallographic refinement method that combines the Rosetta sampling methodology and energy function with reciprocal-space X-ray refinement in Phenix. On a set of difficult low-resolution cases, the method yielded improved model geometry and lower free R factors than alternate refinement methods.
November 2013: Nature Methods
https://www.readbyqxmd.com/read/23975356/improved-chemical-shift-based-fragment-selection-for-cs-rosetta-using-rosetta3-fragment-picker
#20
Robert Vernon, Yang Shen, David Baker, Oliver F Lange
A new fragment picker has been developed for CS-Rosetta that combines beneficial features of the original fragment picker, MFR, used with CS-Rosetta, and the fragment picker, NNMake, that was used for purely sequence based fragment selection in the context of ROSETTA de-novo structure prediction. Additionally, the new fragment picker has reduced sensitivity to outliers and other difficult to match data points rendering the protocol more robust and less likely to introduce bias towards wrong conformations in cases where data is bad, missing or inconclusive...
October 2013: Journal of Biomolecular NMR
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