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MPSA 2004 Final Report

Description: This proposal was to support a portion of the costs of Methods in Protein Structure Analysis 2004 (MPSA2004). MPSA2004 was the 15th in the series of MPSA international conferences on protein structure analysis that began in 1974. MPSA2004 was held on the campus of the University of Washington, Seattle, WA August 29 through September 2, 2004. Twenty-four internationally recognized speakers gave invited presentations; additional participants were chosen to present short talks in the 10 topics that were addressed. The aim of MPSA conferences is to communicate the latest, cutting-edge techniques in protein structure analysis and proteomics through science success stories as told by the scientific leaders who developed the technologies. Biotechnology vendors are present to explain currently available commercial technology through workshops and demonstrations booths. The overall aim is to provide a forum for exchanging the latest methods and ideas in protein structure analysis and proteomics to current and future practitioners. The conference supported the missions of the DOE Office of Science and the Office of Biological and Environmental Research (BER) in at least two ways: by enabling the above forum, and by encouraging young researchers who might otherwise not attend to meet leading researchers and to learn about the most current ideas, technologies, products, and services relevant to protein structure analysis. Topics covered in MPSA2004 were highly relevant to the BER Genomics: GTL initiative and several National Laboratory scientists were among the invited speakers.
Date: February 18, 2006
Creator: Anderson, Carl W.
Partner: UNT Libraries Government Documents Department

The interfacial bioscience grand challenge.

Description: This report is broken down into the following 3 sections: (1) Chemical Cross-linking and Mass Spectrometry Applied to Determination of Protein Structure and Dynamics; (2) Computational Modeling of Membrane Protein Structure and Dynamics; and (3) Studies of Toxin-Membrane Interactions using Single Molecule Biophysical Methods.
Date: March 1, 2004
Creator: Lane, Pamela; Stevens, Mark Jackson; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Crozier, Paul Stewart et al.
Partner: UNT Libraries Government Documents Department

Data growth and its impact on the SCOP database: new developments

Description: The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structuresby their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.
Date: November 13, 2007
Creator: Chandonia, John-Marc; Andreeva, Antonina; Howorth, Dave; Chandonia, John-Marc; Brenner, Steven E.; Hubbard, Tim J.P. et al.
Partner: UNT Libraries Government Documents Department

Structure and Function of Microbial Metal-Reduction Proteins

Description: In this project, we proposed (i) identification of metal-reduction genes, (ii) development of new threading techniques and (iii) fold recognition and structure prediction of metal-reduction proteins. However, due to the reduction of the budget, we revised our plan to focus on two specific aims of (i) developing a new threading-based protein structure prediction method, and (ii) developing an expert system for protein structure prediction.
Date: September 2, 2009
Creator: Xu, Ying; Crawford, Oakly H.; Xu, Dong; Larimer, Frank W.; Uberbacher, Edward C. & Zhou, Jizhong
Partner: UNT Libraries Government Documents Department

Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene

Description: In the protein 4.1R gene, alternative first exons splice differentially to alternative 3' splice sites far downstream in exon 2'/2 (E2'/2). We describe a novel intrasplicing mechanism by which exon 1A (E1A) splices exclusively to the distal E2'/2 acceptor via two nested splicing reactions regulated by novel properties of exon 1B (E1B). E1B behaves as an exon in the first step, using its consensus 5' donor to splice to the proximal E2'/2 acceptor. A long region of downstream intron is excised, juxtaposing E1B with E2'/2 to generate a new composite acceptor containing the E1B branchpoint/pyrimidine tract and E2 distal 3' AG-dinucleotide. Next, the upstream E1A splices over E1B to this distal acceptor, excising the remaining intron plus E1B and E2' to form mature E1A/E2 product. We mapped branch points for both intrasplicing reactions and demonstrated that mutation of the E1B 5' splice site or branchpoint abrogates intrasplicing. In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. More generally, intrasplicing represents a new mechanism whereby alternative promoters can be coordinated with downstream alternative splicing.
Date: November 7, 2008
Creator: Conboy, John G.; Parra, Marilyn K.; Tan, Jeff S.; Mohandas, Narla & Conboy, John G.
Partner: UNT Libraries Government Documents Department

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Description: Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.
Date: September 2, 2007
Creator: Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol et al.
Partner: UNT Libraries Government Documents Department

Optimizing an emperical scoring function for transmembrane protein structure determination.

Description: We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.
Date: October 1, 2003
Creator: Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne & Kolda, Tamara Gibson
Partner: UNT Libraries Government Documents Department

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

Description: We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.
Date: July 20, 2009
Creator: Hura, Greg L.; Menon, Angeli L.; Hammel, Michal; Rambo, Robert P.; Poole II, Farris L.; Tsutakawa, Susan E. et al.
Partner: UNT Libraries Government Documents Department

Method for Sampling Alpha-Helical Protein Backbones

Description: We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible 3-D arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case the method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for 4 of the 25 proteins. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (0.02%--82%) within 6A of the native structure. The method's speed and efficiency make it a valuable contribution towards the goal of predicting protein structure.
Date: February 22, 2000
Creator: Fain, Boris & Levitt, Michael
Partner: UNT Libraries Government Documents Department

Invariant patterns in crystal lattices: Implications for protein folding algorithms

Description: Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist invariants across lattices related to fundamental properties of the protein folding process. This paper considers whether performance-guaranteed approximability is such an invariant for HP lattice models. The authors define a master approximation algorithm that has provable performance guarantees provided that a specific sublattice exists within a given lattice. They describe a broad class of crystal lattices that are approximable, which further suggests that approximability is a general property of HP lattice models.
Date: June 1, 2000
Partner: UNT Libraries Government Documents Department

Manipulating and Visualizing Proteins

Description: ProteinShop Gives Researchers a Hands-On Tool for Manipulating, Visualizing Protein Structures. The Human Genome Project and other biological research efforts are creating an avalanche of new data about the chemical makeup and genetic codes of living organisms. But in order to make sense of this raw data, researchers need software tools which let them explore and model data in a more intuitive fashion. With this in mind, researchers at Lawrence Berkeley National Laboratory and the University of California, Davis, have developed ProteinShop, a visualization and modeling program which allows researchers to manipulate protein structures with pinpoint control, guided in large part by their own biological and experimental instincts. Biologists have spent the last half century trying to unravel the ''protein folding problem,'' which refers to the way chains of amino acids physically fold themselves into three-dimensional proteins. This final shape, which resembles a crumpled ribbon or piece of origami, is what determines how the protein functions and translates genetic information. Understanding and modeling this geometrically complex formation is no easy matter. ProteinShop takes a given sequence of amino acids and uses visualization guides to help generate predictions about the secondary structures, identifying alpha helices and flat beta strands, and the coil regions that bind them. Once secondary structures are in place, researchers can twist and turn these pre-configurations until they come up with a number of possible tertiary structure conformations. In turn, these are fed into a computationally intensive optimization procedure that tries to find the final, three-dimensional protein structure. Most importantly, ProteinShop allows users to add human knowledge and intuition to the protein structure prediction process, thus bypassing bad configurations that would otherwise be fruitless for optimization. This saves compute cycles and accelerates the entire process, so that more and larger problems can be attempted. Currently, the program designers ...
Date: December 5, 2003
Creator: Simon, Horst D.
Partner: UNT Libraries Government Documents Department

Developing Research Capabilities in Energy Biosciences: Design principles of photosynthetic biofuel production.

Description: The current fossil fuel-based energy infrastructure is not sustainable. Solar radiation is a plausible alternative, but realizing it as such will require significant technological advances in the ability to harvest light energy and convert it into suitable fuels. The biological system of photosynthesis can carry out these reactions, and in principle could be engineered using the tools of synthetic biology. One desirable implementation would be to rewire the reactions of a photosynthetic bacterium to direct the energy harvested from solar radiation into the synthesis of the biofuel H2. Proposed here is a series of experiments to lay the basic science groundwork for such an attempt. The goal is to elucidate the transcriptional network of photosynthesis using a novel driver-reporter screen, evolve more robust hydrogenases for improved catalysis, and to test the ability of the photosynthetic machinery to directly produce H2 in vivo. The results of these experiments will have broad implications for the understanding of photosynthesis, enzyme function, and the engineering of biological systems for sustainable energy production. The ultimate impact could be a fundamental transformation of the world's energy economy.
Date: June 30, 2012
Creator: Brown, Donald D. & Savage, David
Partner: UNT Libraries Government Documents Department

Structural Studies of MJ1529, an O6-methylguanine-DNAMethyltransferase

Description: The structure of an O{sub 6}-methylguanine methyltransferase from the thermophile Methanococcus jannaschii has been determined using multinuclear multidimensional NMR spectroscopy. The structure is similar to homologues from other organisms that have been determined by crystallography, with some variation in the N-terminal domain. The C-terminal domain is more highly conserved in both sequence and structure. Regions of the protein show broadening reflecting conformational flexibility that is likely related to function.
Date: January 10, 2006
Creator: Roberts, Anne; Pelton, Jeffrey G. & Wemmer, David E.
Partner: UNT Libraries Government Documents Department

Ancient nature of alternative splicing and functions of introns

Description: Using four genomes: Chamydomonas reinhardtii, Agaricus bisporus, Aspergillus carbonarius, and Sporotricum thermophile with EST coverage of 2.9x, 8.9x, 29.5x, and 46.3x respectively, we identified 11 alternative splicing (AS) types that were dominated by intron retention (RI; biased toward short introns) and found 15, 35, 52, and 63percent AS of multiexon genes respectively. Genes with AS were more ancient, and number of AS correlated with number of exons, expression level, and maximum intron length of the gene. Introns with tendency to be retained had either stop codons or length of 3n+1 or 3n+2 presumably triggering nonsense-mediated mRNA decay (NMD), but introns retained in major isoforms (0.2-6percent of all introns) were biased toward 3n length and stop codon free. Stopless introns were biased toward phase 0, but 3n introns favored phase 1 that introduced more flexible and hydrophilic amino acids on both ends of introns which would be less disruptive to protein structure. We proposed a model in which minor RI intron could evolve into major RI that could facilitate intron loss through exonization.
Date: March 21, 2011
Creator: Zhou, Kemin; Salamov, Asaf; Kuo, Alan; Aerts, Andrea & Grigoriev, Igor
Partner: UNT Libraries Government Documents Department

Report on three Genomes to Life Workshops: Data Infrastructure, Modeling and Simulation, and Protein Structure Prediction

Description: On July 22, 23, 24, 2003, three one day workshops were held in Gaithersburg, Maryland. Each was attended by about 30 computational biologists, mathematicians, and computer scientists who were experts in the respective workshop areas The first workshop discussed the data infrastructure needs for the Genomes to Life (GTL) program with the objective to identify gaps in the present GTL data infrastructure and define the GTL data infrastructure required for the success of the proposed GTL facilities. The second workshop discussed the modeling and simulation needs for the next phase of the GTL program and defined how these relate to the experimental data generated by genomics, proteomics, and metabolomics. The third workshop identified emerging technical challenges in computational protein structure prediction for DOE missions and outlining specific goals for the next phase of GTL. The workshops were attended by representatives from both OBER and OASCR. The invited experts at each of the workshops made short presentations on what they perceived as the key needs in the GTL data infrastructure, modeling and simulation, and structure prediction respectively. Each presentation was followed by a lively discussion by all the workshop attendees. The following findings and recommendations were derived from the three workshops. A seamless integration of GTL data spanning the entire range of genomics, proteomics, and metabolomics will be extremely challenging but it has to be treated as the first-class component of the GTL program to assure GTL's chances for success. High-throughput GTL facilities and ultrascale computing will make it possible to address the ultimate goal of modern biology: to achieve a fundamental, comprehensive, and systematic understanding of life. But first the GTL community needs to address the problem of the massive quantities and increased complexity of biological data produced by experiments and computations. Genome-scale collection, analysis, dissemination, and modeling of those ...
Date: September 16, 2003
Creator: Geist, GA
Partner: UNT Libraries Government Documents Department

Update on the Pfam5000 Strategy for Selection of StructuralGenomics Targets

Description: Structural Genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good financial value, and tractable. In 2003, we presented the ''Pfam5000'' strategy, which involves selecting the 5,000 most important families from the Pfam database as sources for targets. In this update, we show that although both the Pfam database and the number of sequenced genomes have increased in size, the expected benefits of the Pfam5000 strategy have not changed substantially. Solving the structures of proteins from the 5,000 largest Pfam families would allow accurate fold assignment for approximately 65 percent of all prokaryotic proteins (covering 54 percent of residues) and 63 percent of eukaryotic proteins (42 percent of residues). Fewer than 2,300 of the largest families on this list remain to be solved, making the project feasible in the next five years given the expected throughput to be achieved in the production phase of the Protein Structure Initiative.
Date: June 27, 2005
Creator: Chandonia, John-Marc & Brenner, Steven E.
Partner: UNT Libraries Government Documents Department

From photons to protons in the photocycle of bacterial reaction center

Description: The detailed knowledge of the atomic coordinates of the bacterial reaction center (RC) has permitted a close scrutiny of structure/function relationships not only of the quinones but of the protein itself with its internal water structure. Protonatable groups were identified as intrinsic part of the redox reactions, providing charge compensation and forming channels for the movement of hydrogen ions to QB2-. The nature and position of these groups give rise to electrostatic profiles that determine the kinetics and energetics of proton transport. Fine tuning or dramatic variations of protein delivery pathways can adapt the photocycle to changes in bulk phase pH value, buffering capacities and primary structure of the RC.
Date: December 31, 1995
Creator: Maroti, P., Osvath, S., Tapai, C., Hanson, D.K.
Partner: UNT Libraries Government Documents Department

Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal

Description: This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.
Date: August 9, 1996
Creator: Hart, W.E. & Istrail, S.
Partner: UNT Libraries Government Documents Department

Protein Structure Prediction with Evolutionary Algorithms

Description: Evolutionary algorithms have been successfully applied to a variety of molecular structure prediction problems. In this paper we reconsider the design of genetic algorithms that have been applied to a simple protein structure prediction problem. Our analysis considers the impact of several algorithmic factors for this problem: the confirmational representation, the energy formulation and the way in which infeasible conformations are penalized, Further we empirically evaluated the impact of these factors on a small set of polymer sequences. Our analysis leads to specific recommendations for both GAs as well as other heuristic methods for solving PSP on the HP model.
Date: February 8, 1999
Creator: Hart, W.E.; Krasnogor, N.; Pelta, D.A. & Smith, J.
Partner: UNT Libraries Government Documents Department