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Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)
Showing 101 to 200 of 218 items.  Page: 2

Allosteric Mechanism of Hexameric E. coli Arginine Repressor

Rebecca Strawn, Milan Melichercik, Michael Green, Thomas Stockner, Jannette Carey, Rudiger Ettrich

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Allostery in tRNA Synthetases elucidated from MD simulations and Protein Structure Networks

Amit Ghosh, Priti Hansia, Saraswathi Vishveshwara

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Analysis of Structure-Functional Relationships of Adenosine Receptor A2a

Swapna Ravikumar, R. Malathi

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Catalytic Partnership Between Inteins and Their Extein Neighbors

Gil Amitai, Brian P. Callahan, Matt Stanger, Georges Belfort, Marlene Belfort,

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CoMFA and CoMSIA ? A 3D Quantitative Structure Activity Relationship Prediction on Benzodipyrazoles Series as Cyclin Dependent Kinase 2 (CDK2) Inhibitors

Sanjeev K. Singh, Sunil Tripathi, Nigus Dessalew

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Common Structural Motifs of the HIV-1 V3 Variable Loops As the Weak Units in the Virus Protection System

Alexander M. Andrianov, Ivan V. Anishchenko

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Computational Anti-AIDS Drug Development Based on the Evidence For a Strong Attraction of the HIV-1 V3 Loop to Immunophilins

Alexander M. Andrianov

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Computer-based Design of Protein-Protein Interactions

Gurkan Guntas, Carrie Purbeck, Deanne Sammond, Ziad Eletr, Ramesh Jha, Brian Kuhlman

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Conformation of a Peptide Mimetic of the Fourth Cytoplasmic Loop of the CB1 Cannabinoid Receptor

I.R. Chandrashekaran, Anjali Dike, R. Christy Rani Grace, Lea Pagett, Sudha M. Cowsik, Allyn C. Howlett

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Conserved Water Mediated Inter-Domain Recognition in IMPDH-II (human)

Hridoy R. Bairagya, Bishnu P. Mukhopadhyay

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Digestion of the λ cI Repressor with Various Serine Proteases and Correlation with its Three Dimensional Structure

Atasi Pal, Rajagopal Chattopadhyaya

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Effect of the Nonthermal Extra High Frequency Electromagnetic Waves on the Thermostability of Ligand-DNA Complexes

Armen T. Karapetian, Artak V. Grigoryan, Andranik M. Muradyan, Grigor A. Manukyan, Ara P. Antonyan, Kristine A. Pirumyan

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Expression of M. tuberculosis Fatty Acid Synthase I in M. smegmatis

Halimah Sayahi, Kim DeWeerd, Swamy S. Puttamadappa, Silvana. C. Ngo, William R. Jacobs, Jr, Alexander Shekhtman, John T. Welch

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Heat Shock Affects Functioning of the Yeast Plasma-membrane Pma1 H+-ATPase

Valery V. Petrov

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Helix Docking Dynamics: Interface Plasticity and Conformational Dynamics Contributions to Molecular Recognition within a Ubiquitin/UIM Fusion Protein

Nikolaos G. Sgourakis, Scott A. McCallum, Mayank M. Patel, Angel E. Garcia, and George I. Makhatadze

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How the Protein Sequences Adapt to Function in Varied Temperatures? A Comparative Proteome Analyses of Microorganisms that Live in Varied Temperatures

Boojala Vijay B. Reddy, Raghu P. Metpally

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Identifying Kinetically Stable Proteins via Electrophoresis Methods

Ke Xia, Songjie Zhang, Wilfredo Colón

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Insight into the Conformational Features of the HIV-1 Subtype A V3 Loop for Providing Informational Support to Structure-Based Anti-AIDS Drug Projects

Ivan V. Anishchenko, Alexander M. Andrianov

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Network Robustness and Modularity of Protein Structures in the Identification of Key Residues for Allosteric Communications

Antonio del Sol, Marcos J. Araúzo-Bravo, Ruth Nussinov

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On the Nature of the Protein-Protein Interactions in Cataract

Priya R. Banerjee, Ajay Pande, Jayanti Pande

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Pharmacophoric Analysis and Molecular Docking Studies on Selective Cyclooxygenase-2(COX-2) Inhibitors and Their Hits

Poonam Singh, YamunaDevi S, Sanjeev. K. Singh

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Pushing the Frontiers of Atomic Models for Protein Structure Prediction

Kumkum Jain, Priyanka Dhingra, Sandhya Shenoy, B. Jayaram

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Quinones, lipids, channels and chloride ion ? new insights based on the structure of cyanobacterial photosystem II at 2.9 Å resolution

Albert Guskov , Azat Gabdulkhakov, Matthias Broser, Jan Kern, Athina Zouni, and Wolfram Saenger

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RecA-mediated Cleavage of λ cI Repressor Accepts Repressor Dimers: Probable Role of Prolyl cis-trans Isomerization and Catalytic Involvement of H163, K177, and K232 of RecA

Atasi Pal, Rajagopal Chattopadhyaya,

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Recognition and Allosteric Signaling in DNA Mismatch Repair: MD and GNM Studies on MutS Complexes with DNA and ATP

Susan N. Pieniazek, Manju Hingorani, David L. Beveridge,

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Role of Transmembrane Segment M6 in the Biogenesis and Function of the Yeast Plasma-Membrane Pma1 H+-ATPase

Manuel Miranda-Arango, Juan Pablo Pardo, Valery V. Petrov

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Side-Chain Dynamics in PDZ Domain Structure and Function

Chad M. Petit, Anthony B. Law, Jun Zhang, Ernesto J. Fuentes, Andrew L. Lee

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Simulation of a protein tertiary complex: Study of the Interaction Interface and Conformational Dynamics of Dark State Rhodopsin in complex with Transducin

Nikolaos G. Sgourakis and Angel E. Garcia

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Stability of Bilayer Lipid Membrane Under a Combined Effect of Electric Field and Hydrostatic Pressure

Arakelyan V.B., Gevorgyan H.K., Potikyan G.H.

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Structural and Functional Significance of Polypeptide phi, psi outliers

Harish Balasubramanian, Kenneth Gunasekera, Jannette Carey

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Targeting HER2 Protein for Breast Cancer: Exploring the Chemical Space of Peptidomimetics for HER2 Binding Using Docking Method

Seetharama D. Satyanarayanajois, Sharon Ronald

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The Binding of Citrate Synthase and Malate Dehydrogenase with the Inner Mitochondrial Membrane

Igor G. Morgunov, Svetlana V. Kamzolova

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The Structure and Morphology of Amyloid Fibrils Depend on Protein Disulfide Bonds

Dmitry Kurouski, Igor K. Lednev

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Three-Dimensional Structure of the Escherichia coli F1-ATPase in a Self-inhibited Conformation

Tom Duncan, Gino Cingolani

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Modeling Protein-Protein Interface Interactions as a Means for Predicting Protein-Protein Interaction Partners

Vicente M. Reyes

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Pharmacophore Modeling Using a Reduced Protein Representation as a Tool for Srtucture-Based Protein Function Prediction

Vicente M. Reyes

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Pharmacophore Modeling Using a Reduced Protein Representation: Application to the Prediction of ATP, GTP, Sialic Acid, Retinoic Acid and Heme-Bound and -Unbound Nitric Oxide Binding Proteins

Vicente M. Reyes

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Representing Protein 3D Structures in Spherical Coordinates -- Two Applications: 1. Detection of Invaginations, Protrusions and Potential Ligand Binding Sites; and 2. Separation of Protein Hydrophilic Outer Layer from the Hydrophobic Core

Vicente M. Reyes

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Two Complementary Methods for Quantifying Ligand Binding Site Burial Depth in Proteins: The "Cutting Plane" and the "Tangent Sphere Methods"

Vicente M. Reyes

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A Low-Temperature Thermal Transition for Quadruplex DNAs

Lance M. Hellman, Whitney Tackett, Emily Lawson, Michael G. Fried

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Binding of new Ag-containing porphyrins with DNA. The influence of pH

A. A. Ghazaryan, S. A. A. Sulyman, Y.B. Dalyan

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Binding of Some Antitumour Compounds with the DNA-radiated Millimeter Electromagnetic Waves

Yu. S. Babayan, G.L. Kanaryan, S. Yu. Babayan, P.S. Khazaryan, L.R. Grigoryan

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Cisplatin Action on Content of Neutral Lipids of Rat Liver and Brain Nuclei

Hakobyan N.R., Yavroyan Zh.V., Hovhannisyan A.G., Gevorgyan E.S.

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Cooperative Effect of EtBr on DNA-cis-DDPt Complexes

Poghos O. Vardevanyan, Anush V.Arakelyan, Ara P. Antonyan, Lilit S.Baghdasaryan, Gor S. Sarkisyan

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Different Modes of Hoechst 33258 Binding with Different GC-content DNAs

Poghos O.Vardevanyan, Ara P. Antonyan, Ruzanna A. Karapetian, Marine A. Parsadanyan, Mariam A. Shahinyan

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Dinuclear Ruthenium(II) Complexes as G-Quadruplex DNA

Li Xu, Hui Chao, Liangnian Ji

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DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment

Geoff S. Baldwin, Nicholas J. Brooks, Rebecca E. Robson, Aaron Wynveen, Arach Goldar, Sergey Leikin, John M. Seddon, Alexei A. Kornyshev

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DNA Repair Mutants Of O6-alkylguanine-DNA alkyltransferase (AGT) That Affect DNA Binding Affinity, Cooperativity and Repair

Claire Adams, Michael Fried

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Electrostatic Properties of Promoter and Nonpromoter Sites in T7 Bacteriophage Genome

S. G. Kamzolova, P. M. Beskaravainy, A. A. Sorokin

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Evolutionary Constraint on DNA Structure in the Human Genome

Thomas D. Tullius, Stephen C. J. Parker, Loren Hansen, Hatice Ozel Abaan, Elliott H. Margulies

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Evolutionary Dynamics of CRISPR-Cassettes in the Metagenome Sorcerer II

Irena I. Artamonova, Valery A. Sorokin, Mikhail S. Gelfand

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Finding Faults in DNA Mismatch Repair: Kinetic analysis of MutS actions on DNA

Jie Zhai, Manju M Hingorani,

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Hoechst 33258 Dimers Bind Mainly to dsDNA GC Pairs

S. A. Streltsov

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Influence of Coherent Nonthermal Electromagnetic Radiation on Water and DNA Solution Densities

Yu S. Babayan, V.P. Kalantaryan, A. A. Tadevosyan, G. L. Kanaryan, G. R. Ulikhanyan, S. V. Harutyunyan

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Influence of the Location of a Single Stabilizing Chemical Modification on DNA Internal Melting and Strand Dissociation

Dmitri Y. Lando , Alexander S. Fridman , Elena N. Galyuk, Chin-Kun Hu

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Isoquinoline Alkaloids as Natural Products with Unique DNA Binding Properties

Kakali Bhadra, Gopinatha Suresh Kumar

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Kinetics of DNA Stability in the Presence of Cisplatin and Transplatin

Dmitri Y. Lando , Elena N. Galyuk, Alexander S. Fridman , Chin-Kun Hu

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Minor Groove Shape and Electrostatics Provide a Molecular Origin for Protein-DNA Specificity

Remo Rohs, Sean M. West, Peng Liu, Barry Honig

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Monovalent Cation Binding by DNA Hairpins

Nancy C. Stellwagen, Joseph Muse, Paul Barnard, Earle Stellwagen

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New Insights on Non-specific Protein-DNA Interactions: the DNase I Model

Marc Guéroult, Josephine Abi Ghanem, Brahim Heddi, Chantal Prévost, Pierre Poulain, Marc Baaden, Brigitte Hartmann

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Nucleotide Sequence-Dependent Shape Effects and their Role in Protein-DNA Recognition

Remo Rohs, Barry Honig

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Observation of Oligonucleotide Dynamics By Means of Fluorescent Nucleoside Analog 6MI

Andrew Moreno, Ishita Mukerji, Knee

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Protein-DNA Recognition Mechanism and Prediction

Akinori Sarai

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Regulation of Sin-Mediated DNA Recombination

Kent W. Mouw, Sherwin Montano, Ross Keenholtz, Martin R. Boocock, Sally-J. Rowland, W. Marshall Stark, Phoebe A. Rice

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Selective, High-affinity, Synthetically Accessible Ligands for G-quadruplex DNA: Thermodynamic and Structural Studies of Azacyanines

Aaron E. Engelhart, Özgül Persil Çetinkol, Rupesh K. Nanjunda, W. David Wilson, Nicholas V. Hud.

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Sequence Studies of Promoter Regions in Human Genome

Padmavathi Putta, Chanchal K. Mitra

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Sequence- And Structure-Specific DNA Base-Flipping By AGT

Manana Melikishvili , Michael G. Fried

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Sequence-specific Labeling of Duplex DNA Using Nicking Enzymes and Oligonucleotide Probes

Heiko Kuhn, Katya Protozanova, Gary Jaworski, Rhea Mahabir, Maxim Frank-Kamenetskii

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Single-stranded DNA and RNA binds to a conserved surface of cold-shock domains

Klaas E.A. Max, Udo Heinemann

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Specific Protein-DNA Complexes as Platforms for Design of New Types of Antiviral Drugs

G.V. Gursky, S.L. Grokhovsky, A.N. Surovaya, Y.G. Gursky, V.L. Andronova, N.P. Bazhulina, V.S. Archipova, A.M. Nikitin, G.A. Galegov

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Specific versus Nonspecific DNA Binding of the Restriction Endonuclease EcoRV Measured by Self-Cleavage Assay

Nina Sidorova, Shakir Muradymov, Donald C. Rau

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Stability of right-handed DNA crossovers mediated by divalent cations in solution

Peter Varnai , Youri Timsit

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Stereoselectivelly deuterated nucleosides for NMR studies of DNA

Mark Lukin , Tanya Zaliznyak, Carlos de los Santos

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Structural and Mechanistic Insights into Single-stranded DNA Transposition

Orsolya Barabas, Catherine Guynet , Adeline Achard , Bao Ton-Hoang , Michael Chandler , Fred Dyda, Alison B. Hickman

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Structural Changes and Reaction Intermediates in the Catalytic Cycles of DNA Repair Enzymes

N. A. Kuznetsov, L. Yu. Kanazhevskaya, V. V. Koval, D. O. Zharkov, O. S. Fedorova

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Structural Energetics of a DNA-RNA Hybrid Containing a Tract of dA-rU Base Pairs

Yuegao Huang, Congju Chen, Irina M. Russu

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Temperature-induced Unfolding of Unusual DNA Structures: Correlation of Optical and DSC Melting Curves with Fluorescence Melts Using 2-Aminopurine.

Hui-Ting Lee, Lela Waters, Chris Olsen, Irine Khutsishvili, Luis A. Marky

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The Comparative Study of CuTAlPyP(4) and CoTAlPyP(4) Porphyrins with DNA

G. Ananyan, A. Avetisyan, Y. Dalyan

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The Effect of UV radiation on DNA-cis-DDP Complex

Lusine Abgaryan

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The Role of Conformational Flexibility in Proteins' Search for their Recognition Sites

Jason S. Leith, M. Slutsky, L.A. Mirny

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Uncovering Subtle Effects on Structures of Nucleic Acids in Solution and Protein-bound Forms Through Vibrational Spectroscopy

Spriha Gogia, Hemalatha Balaram, Mrinalini Puranik

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Watson-Crick Recognition of Double-Stranded B-DNA

Danith H. Ly

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A Translational Signature for Nucleosome Positioning In vivo

Micaela Caserta, Eleonora Agricola, Mark Churcher, Edwige Hiriart, Loredana Verdone, Ernesto Di Mauro, Andrew Travers

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Changes in Chromatin Conformation and PARP-1 Activity Induced by Cisplatin in Rat Liver

Artsruni IG, Matinyan KS, Demirkhanyan LH, Gevorgyan ES

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Chromatin higher order structure and regulation of its compaction

Daniela Rhodes, Sara Sandin, Andrew Routh, Philip Robinson

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Determinants of Histone Tail Function during Chromatin Condensation

Jeffrey C. Hansen, Steven J. McBryant, Xu Lu

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Epigenetic silencing in the initiation and progression of human cancer

Stephen B. Baylin

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Graphical Modeling of the Beta-Globin Transcription Factory

Wong H., Mozziconacci J.

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Individualization of Chromatids in Higher Eukaryotes

Zbyszek Otwinowski, Dominika Borek

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Internucleosome Interactions in Chromatin Higher-order Fibers

Sergei A. Grigoryev, Sarah Correll, Christopher L. Woodcock

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Mesoscale Modeling Predicts New Polymorphic Structure of Chromatin

Gaurav Arya, Sergei Grigoryev, Tamar Schlick,

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On the Structure of The 30 nm Chromatin Fibre

D. Staynov

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Recognition of Trimethylated K4 of Histone H3 by the TFIID Subunit TAF3

H. van Ingen, F.M.A. van Schaik, H. Wienk, H. Rehmann, J. Kruijzer, R.M.J. Liskamp, H.Th.M. Timmers, R. Boelens,

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RNA-mediated Epigenetic Mechanism of Genome Rearrangement

Mariusz Nowacki, Vikram Vijayan, Yi Zhou, Thomas G. Doak, Keerthi Shetty, Klaas Schotanus, Laura F. Landweber

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Simulations of Core Histone Modifications on Human Mono Nucleosomes Reveal Alterations in Stability

M. Vijayalakshmi, R. Sowdhamini, G. V. Shivashankar

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Structural Insights Into the Unusual Chemistry of Sir2 Enzymes

Cynthia Wolberger, William Hawse, Kamau Fahie, Kevin Hoff

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Structural Perturbation of Chromatin by Plant Alkaloid Sanguinarine and Its Functional Consequences

Suman Kalyan Pradhan, Ruthrotha Selvi B, Jayasha Shandilya, Chandrima Das, Tapas K. Kundu, Dipak Dasgupta

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Topology of Eukaryotic Chromatin

Dominika Borek, Zbyszek Otwinowski

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A Statistical Thermodynamic Approach for Predicting The Sequence-Dependent Nucleosome Positioning along Genomes

P. De Santis, A. Scipioni

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Architecture and Regulation of the CHD1 Chromatin Remodeler

G. Hauk, J. Mcknight, I. M. Nodelman, G. D. Bowman

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