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Nature 2011年第7335期470卷 472-473页

作者： Barry Honig Remo Rohs Department of Biochemistry and Molecular Biophysics Barry Honig is at the Howard Hughes Medical Institute Center for Computational Biology and Bioinformatics Columbia University New York New York 10032 USA. Department of Biological Sciences Remo Rohs is in the Molecular and Computational Biology Program University of Southern California Los Angeles California 90089 USA.

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Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models

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Journal of structural and Functional Genomics 2011年第2期12卷 137-147页

作者： Zimmermann, Michael T. Leelananda, Sumudu P. Gniewek, Pawel Feng, Yaping Jernigan, Robert L. Kloczkowski, Andrzej Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50011-0320 United States L.H.Baker Center for Bioinformatics and Biological Statistics Iowa State University Ames IA 50011-3020 United States Bioinformatics and Computational Biology Interdepartmental Graduate Program Iowa State University Ames IA 50011 United States Laboratory of Theory of Biopolymers Faculty of Chemistry University of Warsaw 02-093 Warsaw Pasteura 1 Poland Battelle Center for Mathematical Medicine Research Institute at Nationwide Children's Hospital Columbus OH 43205 United States Department of Pediatrics Ohio State University College of Medicine Columbus OH 43205 United States

We propose a novel method of calculation of free energy for coarse grained models of proteins by combining our newly developed multibody potentials with entropies computed from elastic network models of proteins. Multi-body potentials have been of much interest recently because they take into account three dimensional interactions related to residue packing and capture the cooperativity of these interactions in protein structures. Combining four-body non-sequential, four-body sequential and pairwise short range potentials with optimized weights for each term, our coarse-grained potential improved recognition of native structure among misfolded decoys, outperforming all other contact potentials for CASP8 decoy sets and performance comparable to the fully atomic empirical DFIRE potentials. By combing statistical contact potentials with entropies from elastic network models of the same structures we can compute free energy changes and improve coarse-grained modeling of protein structure and dynamics. The consideration of protein flexibility and dynamics should improve protein structure prediction and refinement of computational models. This work is the first to combine coarse-grained multibody potentials with an entropic model that takes into account contributions of the entire structure, investigating native-like decoy selection. © 2011 Springer Science+Business Media B.V.

关键词： 4-Body potentials Elastic network models Multibody potentials Protein dynamics Protein structure prediction Protein structure refinement

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Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays

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BMC Research Notes 2010年第1期3卷 1-18页

作者： Guo, Beibei Villagran, Alejandro Vannucci, Marina Wang, Jian Davis, Caleb Man, Tsz-Kwong Lau, Ching Guerra, Rudy Department of Statistics Rice University Houston TX 77005-1827 6100 Main United States Department of Statistics University of Connecticut Storrs CT 06269-4120 United States Department of Pediatrics Baylor College of Medicine Texas Children's Hospital Houston TX 77030 6621 Fannin St. United States Structural and Computational Biology and Molecular Biophysics Program Baylor College of Medicine Houston TX 77030 One Baylor Plaza United States

Background. The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarrays. The method is based on a Bayesian spatial normal mixture model with an unknown number of components corresponding to true copy numbers. A reversible jump Markov chain Monte Carlo algorithm is used to implement the model and perform posterior inference. Results. The performance of the algorithm is examined on both simulated and real cancer data, and it is compared with the popular CNAG algorithm for copy number detection. Conclusions. We demonstrate that our Bayesian mixture model performs at least as well as the hidden Markov model based CNAG algorithm and in certain cases does better. One of the added advantages of our method is the flexibility of modeling normal cell contamination in tumor samples. © 2010 Guerra et al;licensee BioMed Central Ltd.

关键词： Comparative Genomic Hybridization Misclassification Rate Copy Number Aberration Normal Copy Number Reversible Jump Markov Chain Monte Carlo

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Efficient and Stereoselective Synthesis of α(2→9) Oligosialic Acids: From Monomers to Dodecamers†

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Angewandte Chemie 2011年第40期123卷

作者： Kuo‐Ching Chu Chien‐Tai Ren Chun‐Ping Lu Che‐Hsiung Hsu Tsung‐Hsien Sun Jeng‐Liang Han Bikash Pal Tsung‐An Chao Yung‐Feng Lin Shih‐Hsiung Wu Chi‐Huey Wong Chung‐Yi Wu Genomics Research Center Academia Sinica 128 Academia Road Section 2 Nankang Taipei 115 (Taiwan) Institute of Biological Chemistry Academia Sinica (Taiwan) Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Academia Sinica 128 Academia Road Section 2 Nankang Taipei 115 (Taiwan) Institute of Bioinformatics and Structural Biology National Tsing‐Hua University Hsin‐Chu (Taiwan)

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Auf dem Weg zur automatisierten Oligosaccharid‐ Synthese

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Angewandte Chemie 2011年第50期123卷

作者： Che‐Hsiung Hsu Shang‐Cheng Hung Chung‐Yi Wu Chi‐Huey Wong The Genomics Research Center Academia Sinica Taiwan 128 Academia Road Section 2 Nankang Taipei 115 (Taiwan) Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Academia Sinica (Taiwan) Institute of Bioinformatics and Structural Biology National Tsing‐Hua University Hsin‐Chu (Taiwan) Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 (USA)

Kohlenhydrate spielen eine wichtige Rolle bei biologischen Vorgängen. Das Fortschrittstempo der Kohlenhydratforschung ist jedoch relativ langsam, was unter anderem mit der Komplexität der Kohlenhydratstrukturen und dem Fehlen allgemein anwendbarer Synthesemethoden und Verfahren zur Untersuchung dieser Klasse von Biomolekülen zusammenhängt. Jüngste Fortschritte in der Synthese haben ergeben, dass viele dieser Probleme umgangen werden können. In diesem Aufsatz beschreiben wir die Methoden, die entwickelt wurden, um mit den Herausforderungen kohlenhydratvermittelter biologischer Vorgänge umzugehen. Besonderes Augenmerk wird dabei auf die Entwicklung der automatisierten Synthese von Oligosacchariden gerichtet. Darüber hinaus werden auch Kohlenhydrat‐Mikroarrays und Impfstoffe auf Kohlenhydratbasis behandelt.

关键词： Eintopfreaktionen Festphasensynthese Impfstoffe Kohlenhydrate Mikroarrays

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Characterization of the retinal proteome during rod photoreceptor genesis

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BMC Research Notes 2010年第1期3卷 1-8页

作者： Barnhill, Alison E Hecker, Laura A Kohutyuk, Oksana Buss, Janice E Honavar, Vasant G Greenlee, Heather West Interdepartmental Neuroscience Program Iowa State University Ames IA United States Department of Biomedical Sciences Iowa State University Ames IA United States Bioinformatics and Computational Biology Program Iowa State University Ames IA United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA United States Department of Computer Science Iowa State University Ames IA United States National Animal Disease Center Ames IA 50010 United States Mayo Clinic Department of Ophthalmology Rochester MN 55905 United States

Background. The process of rod photoreceptor genesis, cell fate determination and differentiation is complex and multi-factorial. Previous studies have defined a model of photoreceptor differentiation that relies on intrinsic changes within the presumptive photoreceptor cells as well as changes in surrounding tissue that are extrinsic to the cell. We have used a proteomics approach to identify proteins that are dynamically expressed in the mouse retina during rod genesis and differentiation. Findings. A series of six developmental ages from E13 to P5 were used to define changes in retinal protein expression during rod photoreceptor genesis and early differentiation. Retinal proteins were separated by isoelectric focus point and molecular weight. Gels were analyzed for changes in protein spot intensity across developmental time. Protein spots that peaked in expression at E17, P0 and P5 were picked from gels for identification. There were 239 spots that were picked for identification based on their dynamic expression during the developmental period of maximal rod photoreceptor genesis and differentiation. Of the 239 spots, 60 of them were reliably identified and represented a single protein. Ten proteins were represented by multiple spots, suggesting they were post-translationally modified. Of the 42 unique dynamically expressed proteins identified, 16 had been previously reported to be associated with the developing retina. Conclusions. Our results represent the first proteomics study of the developing mouse retina that includes prenatal development. We identified 26 dynamically expressed proteins in the developing mouse retina whose expression had not been previously associated with retinal development. © 2010 Greenlee et al.;licensee BioMed Central Ltd.

关键词： Protein Spot Mouse Retina Retinal Development Retinal Protein Probability Base Mowse Score

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Microano-fabrication technologies for cell biology

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Medical & Biological Engineering & Computing 2010年第10期48卷 1023-1032页

作者： Qian, Tongcheng Wang, Yingxiao Department of Bioengineering and the Beckman Institute for Advanced Science and Technology University of Illinois at Urbana–Champaign Urbana USA Department of Biomedical Engineering Peking University Beijing People’s Republic of China Department of Integrative and Molecular Physiology Center for Biophysics and Computational Biology Institute for Genomic Biology Neuroscience Program University of Illinois at Urbana–Champaign Urbana USA

Micro/nano-fabrication techniques, such as soft lithography and electrospinning, have been well-developed and widely applied in many research fields in the past decade. Due to the low costs and simple procedures, these techniques have become important and popular for biological studies. In this review, we focus on the studies integrating micro/nano-fabrication work to elucidate the molecular mechanism of signaling transduction in cell biology. We first describe different micro/nano-fabrication technologies, including techniques generating three-dimensional scaffolds for tissue engineering. We then introduce the application of these technologies in manipulating the physical or chemical micro/nano-environment to regulate the cellular behavior and response, such as cell life and death, differentiation, proliferation, and cell migration. Recent advancement in integrating the micro/nano-technologies and live cell imaging are also discussed. Finally, potential schemes in cell biology involving micro/nano-fabrication technologies are proposed to provide perspectives on the future research activities.

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Late Residual γ-H2AX Foci In Murine Skin are Dose Responsive and Predict Radiosensitivity In Vivo. (vol 172, pg 1, 2010)

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RADIATION RESEARCH 2010年第3期173卷 399-400页

作者： Bhogal, N. Kaspler, P. Jalali, F. Hyrien, O. Chen, R. Hill, R. P. Bristow, R. G. [a]Applied Molecular Oncology and Radiation Medicine Program Ontario Cancer Institute/Princess Margaret Hospital (UHN) Toronto Ontario Canada [b]Department of Biostatistics and Computational Biology University of Rochester Medical Center Rochester New York [c]Departments of Medical Biophysics and Radiation Oncology University of Toronto Toronto Ontario Canada Bhogal N. Kaspler P. Jalali F. Hyrien O. Chen R. Hill R. P. and Bristow R. G. Late Residual γ-H2AX Foci In Murine Skin are Dose Responsive and Predict Radiosensitivity In Vivo.

Accurate biodosimetry is needed to estimate radiation doses received in vivo from accidental or unwarranted radiation exposures. We investigated the use of DNA repair foci (e.g. γ-H2AX) at late times after irradiation in vivo as a biodosimeter of initial ionizing radiation dose. Two radiosensitive strains (SCID and BALB/c) and two radioresistant strains (C57BL/6 and C3H/HeJ) were used to quantify γ-H2AX foci in a skin tissue microarray after doses of 1 to 10 Gy at early and late times after irradiation (1 and 7 days). Using a 3D quantitative immunofluorescence microscopy analysis, we observed a dose response for γ-H2AX foci for all strains at 30 min, 24 h and 7 days after irradiation. The numbers of residual foci were significantly different between each of the four strains and reflected the relative radiosensitivity in vivo. In comparing γ-H2AX focus and micronucleus formation after irradiation, we also observed association between the number of micronuclei and number of foci after 1 and 7 days between radiosensitive and radioresistant strains. We conclude that 3D image analysis of γ-H2AX in skin can be used to detect relative radiosensitivity based on late residual γ-H2AX foci. This technique may be a useful biodosimeter to determine dose at times up to 1 week after accidental or catastrophic radiation exposure in vivo.

关键词： Skin Dose response relationship Irradiation Epidermal cells Radiotherapy DNA repair Radiation dose response relationship Mice Biopsies

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Kinetics of Conformational Sampling in Ubiquitin†

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Angewandte Chemie 2011年第48期123卷

作者： David Ban Michael Funk Rudolf Gulich Dalia Egger T. Michael Sabo Korvin F. A. Walter R. Bryn Fenwick Karin Giller Fabio Pichierri Bert L. de Groot Oliver F. Lange Helmut Grubmüller Xavier Salvatella Martin Wolf Alois Loidl Reiner Kree Stefan Becker Nils‐Alexander Lakomek Donghan Lee Peter Lunkenheimer Christian Griesinger Department of NMR‐based Structural Biology Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen (Germany) Experimental Physics V University of Augsburg Universitätsstraße 2 86135 Augsburg (Germany) Laboratory of Molecular Biophysics ICREA and Institute for Research in Biomedicine Barcelona Parc Cientific de Barcelona C/Baldiri Reixac 10 08028 Barcelona (Spain) G‐COE Laboratory Department of Applied Chemistry Tohoku University 980‐8579 Sendai (Japan) Department of Theoretical and Computational Biophysics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen (Germany) Department of Theoretical Physics University of Göttingen Friedrich‐Hund‐Platz 1 37077 Göttingen (Germany)

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Redesign of high-affinity nonspecific nucleases with altered sequence preference

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Journal of the American Chemical Society 2009年第47期131卷 17345-17353页

作者： Wang, Yi-Ting Wright, Jon D. Doudeva, Lyudmila G. Jhang, Hua-Ci Lim, Carmay Yuan, Hanna S. Institute of Molecular Biology Academia Sinica Taipei Taiwan Institute of Biomedical Sciences Academia Sinica Taipei Taiwan Institute of Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Academia Sinica Taipei Taiwan Institute of Bioinformatics and Structural Biology Department of Chemistry National Tsing Hua University HsinChu Taiwan Institute of Biochemistry and Molecular Biology National Taiwan University Taipei Taiwan

It is of crucial importance to elucidate the underlying principles that govern the binding affinity and selectivity between proteins and DNA. Here we use the nuclease domain of Colicin E7 (nColE7) as a model system to generate redesigned nucleases with improved DNA-binding affinities. ColE7 is a bacterial toxin, bearing a nonspecific endonuclease domain with a preference for hydrolyzing DNA phosphodiester bonds at the 3O-side after thymine and adenine;i.e., it prefers Thy and Ade at the -1 site. Using systematic computational screening, six nColE7 mutants were predicted to bind DNA with high affinity. Five of the redesigned single-point mutants were constructed and purified, and four mutants had a 3- to 5-fold higher DNA binding affinity than wild-type nColE7 as measured by fluorescence kinetic assays. Moreover, three of the designed mutants, D493N, D493Q, and D493R, digested DNA with an increased preference for guanine at +3 sites compared to the wild-type enzyme, as shown by DNA footprint assays. X-ray structure determination of the ColE7 mutant D493Q-DNA complex in conjunction with structural and free energy decomposition analyses provides a physical basis for the improved protein-DNA interactions: Replacing D493 at the protein-DNA interface with an amino acid residue that can maintain the native hydrogen bonds removes the unfavorable electrostatic repulsion between the negatively charged carboxylate and DNA phosphate groups. These results show that computational screening combined with biochemical, structural, and free energy analyses provide a useful means for generating redesigned nucleases with a higher DNA-binding affinity and altered sequence preferences in DNA cleavage. © 2009 American Chemical Society.

关键词： DNA

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