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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001
Showing 1 to 100 of 223 items.  Page: 1 3

2-aminopurine as a Probe for Parallel or Antiparallel Orientation

Anna K. Shchyolkina (1), Dmitry N. Kaluzhny (1), Olga F. Borisova (1), Quentin Hanley (2), Andrew Clayton (2), Donna J. Jovin (2), Thomas M. Jovin (2)

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A Comparative Study of DNA Binding to Mg(II) and Ca(II) in Aqueous Solution By Capillary Electrophoresis and FTIR Spectroscopic Methods

H. A. Tajmir-Riahi, H. Arakawa, H. Malonga, R. Ahmad

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A crystallographic map of the transition from B-DNA to A-DNA

Jeffrey M. Vargason(1), Keith Henderson(2), and P. Shing Ho(1,)

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A DNA Nanotube Based on a Six-Helix Bundle Motif

Frederick Mathieu, Chengde Mao and Nadrian C. Seeman

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A Multiple Copy Simulated Annealing Algorithm for Polypeptide Structure Prediction On A Beowulf PC Cluster.

Yongxing Liu and David L. Beveridge

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A NMR Investigation of the Energetics of Allosteric Effects in Human Hemoglobin

Iulian N. Rujan (1), and Irina M. Russu (2),

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A Novel Peptide Inhibitor of HIV-1 Integrase: A Structure-Based Computer Model

Gita Subba Rao, Vivek Ahuja and Sonika Bhatnagar

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A padlock oligonucleotide for labelling plasmids

T. Roulon (1), E. Le Cam (2), T. Garestier (1), C. Helene (1) and C. Escude (1).

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A Quarts Crystal Microbalance Cell Biosensor: Detection of Microtubule Altarations in Living Cells at nM Nocodazole Conceatrations

Kenneth A. Marx, Tiean Zhou, Heather Schulze#, Anne Montrone# and Susan Braunhut#

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A Robust Sequence-Dependent Rotary DNA Nanomechanical Device

Hao Yan, Xiaoping Zhang and Nadrian C. Seeman

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Actinomycin D Binds Strongly to d(TGTCATG) with a 2:1 Drug to DNA Duplex Binding Stoichiometry

Fu-Ming Chen and Feng Sha

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Albany 2001: The 12th Conversation, First Conversation of the Twenty First Century

The Program

Registraion, Reservation of meals and Accommodation

Young Scientist Speaker Program

Financial Assistance

Submission of Abstracts From Lecturers and for Poster Presentation

Abstracts: The Twelfth Conversation

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All coordination sites in the central channel of G-quadruplexes need not be occupied by cations: A 6-nanosecond molecular dynamics study

Shibasish Chowdhury and Manju Bansal

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Ammonium induces a conformational change in the Dickerson dodecamer

K. Snoussi and J.-L. Leroy

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An ab Initio Study of the cis-syn Cyclobutane Pyrimidine Dimers and a Tautomer-Bypass Mechanism for the Origin of UV-Induced Mutations

V. I. Danilov (1), A. Les (2), J. L. Alderfer (3)

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An Investigation of Adenine Recognition in the U1A:U1snRNA Complex

Jacob B. Tuite, Jerome C. Shiels, Scott J. Nolan, Kerry L. Cecere, and Anne M. Baranger

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Analysis of Peptides and Proteins With Electrodes

Emil Palecek, Sabina Billov?, Marie Br?zdov?, Ludek Havran, Rene Kizek and Mirek Tomschik

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Analysis of Triplex DNA Formation in the Promoter Region of Human c-src Proto-Oncogene - A Molecular Beacon Approach

Thomas Antony and Vinod Subramaniam

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Antiparallel DNA Loop in Gal Repressosome

Victor B. Zhurkin, Mark Geanacopoulos, George Vasmatzis and Sankar Adhya

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Apoptosis, Cell Senescence And Telomere Shortening Induced By Specific Quadruplex Dna Ligands

Mergny, J.L.(1) , Guittat, L.(1) ; Riou, J.F.(2); Teulade-Fichou, M.P.(3), Alberti, P.(1) , Hounsou, C.(3), François, J.C.(1) , Mailliet, P.(2); Laoui, A.(2); Lacroix, L.(1) , Vigneron, J.P.(3), Lehn, J.M.(3), Garestier, T.(1) and Hélène, C.(1)

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Approximate Dynamics of DNA, the 11 nm and 30 nm fibers

Thomas C. Bishop and Oleksandr O. Zhmudsky

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Archaeal histone-fold protein HMf creates bona fide chromatin fibers

Tomschik, M., Karymov, M.A., Zlatanova, J. and Leuba, S.H.

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Architecture of H-Type Pseudoknots and The Role Of Pseudknots in Frameshifting

H.A. Heus(1), Paul J.A. Michiels(1), Alexandra A.M. Versleijen(1), Cornelis W.A. Pleij(2) & Cornelis W. Hilbers(1),

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Artificial Primosome

Irina V. Smolina, Natalia E. Broude, Heiko Kuhn, Maxim D. Frank-Kamenetskii and Vadim V. Demidov

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Association of yeast inosine 5'-monophosphate dehydrogenase with a fragment of the C-rich telomeric strand

Jean-Fran?ois Cornuel, Anne Moraillon and Maurice Gu?ron

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Atomic-Resolution Picture of Structure and Dynamics of G-DNA and Other Unusual DNA Molecules. Large-Scale Molecular Dynamics Simulations.

Nada Spackova (1), Richard Stefl (2), Imre Berger (3), Jaroslav Koca (2), and Jiri Sponer (1)

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Binary DNA Tracts can serve as DNA Unwinding Centers.

Gad Yagil,

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Binding of Actinomycin D to Single-stranded DNA of Sequence Motifs d(TGTCTnG) and d(TGTnGTC).

Fu-Ming Chen and Feng Sha

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Binding of Latent and Activated Protein p53 to Supercoiled and Chemically Damaged DNA

Miroslav Fojta, Marie Brazdova, Pavlina Becvarova, Jan Palecek, Sarka Pospisilova, Borivoj Vojtesek and Emil Palecek

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Binding of p53 Protein to Double-Stranded DNA

Dmitry I. Cherny (1), Marie Brazdova (2), Jan Palecek (2), Emil Palecek (2) and Thomas M. Jovin (1)

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Binding of p53 Protein to Supercoiled DNA

J. Palecek(1), M. Brazdova(1), M.Fojta(1), D. Cherny(3), E. Jagelska(1), P. Pecinka(1), S. Billova(1), L. Karlovska(1), V. Brazda(1), S. Pospisilova(2), B. Vojtesek(2), V. Subramaniam(3), T. Jovin(3) and E. Palecek(1)

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Biochemical and Structural Investigation of the Sequence-Specific Binding Interaction between the Yeast Protein Cdc13p and Single-Stranded Telomeric DNA

Deborah S. Wuttke

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Biochemical evidence for base flip-out in DNA containing biologically-relevant levels of positive supercoiling

Marita Barth and Peter Dedon,

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Biology-based nanoelectronics: Self-assembly of devices and networks by recombinant DNA

Erez Braun, Uri Sivan, Kinneret Keren, Yoav Soen and Gdalyahu Ben-Yoseph

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Calculated myosin motions with coarse-grained models

Isabelle Navizet and Robert Jernigan

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Calculation of DNA Condensation Caused by Ligand Binding Using a Two-State Model

Vladimir B. Teif, Vladimir I. Vorob'ev and Dmitri Y. Lando

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Calorimetric Studies of Domain Interactions in HIV-1 Capsid Protein

Irina I. Protassevitch (1,2), Jason Lanman (1) and Peter E. Prevelige Jr (1)

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CD Evidence that Ff g5p Selectively Binds to the Structured Form of a G-rich DNA Oligomer in the Presence of Sodium Ion.

Jin-Der Wen and Donald M. Gray

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Cellular Signaling by Tyrosine Phosphorylation

J. Schlessinger

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Cellular Uptake Characteristics of DNA Frayed Wires

Micheline Piquette-Miller, Won-Sang Lee, Robert B. Macgregor, Jr.

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Characterization of the peptide-receptive form of the human class II major histocompatibility complex HLA-DR1.

Zarixia Zavala-Ruiz, Jennifer Zarutskie, and Lawrence J. Stern.

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Chiral Self-Assemblies of Hematoporphyrin IX Derivatives in Tissue

Robert Bischoff (1), Gerlinde Bischoff (2), Siegfried Hoffmann (2), SENSOBI Sensoren GmbH (1),, Weinbergweg 22, 06120 Halle, Germany, bischoff@sensobi.de

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Chromatin Dynamics

Ariel Prunell

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Chromo domain of Drosophila HP1 interacts specifically with the N-terminal tail of histone H3 methylated at Lysine 9

Steven A. Jacobs, Sean D. Taverna, Yinong Zhang, Jinmei Li, C. David Allis, & Sepideh Khorasanizadeh

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Classification of CD and absorption spectra in the Soret band of H2TMPyP bound to various synthetic polynucleotides

Sun-Hee Jeon(1), Soo-min Lee(1), Bok-Jo Kim(2), Sung-Wook Han(2) and Seog K. Kim(1)

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Columnar Structure Of Telomeric Chromatin

Jiri Fajkus (1) and Edward N. Trifonov (2), Dept of Functional Genomics (1), Inst. of Biophysics, Acad. of Sci of the Czech Republic and Masaryk Uni. Brno, Kralovopolska 135,

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Combinatorial Libraries of Porphyrin Derivatives: Finding G-quadruplex: Interactive Agents With a High Specificity for Human Telomeric Repeats

Jonathan Feig, Yosry Hussein and James S. Godde

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Comparative and ab initio three dimensional models of the carboxy terminal domain of the lambda repressor and their use to build intact repressor tetramer models bound to adjacent operator sites

Rajagopal Chattopadhyaya and Kaushik Ghosh

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Comparison Between the Simulated Melting and the Average Mutual Information of DNA Sequences

Dang D. Long , Kenneth A. Marx , and Ivo Grosseà.

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Competition Between Different Ligand-DNA Complexes Produces S-shaped Binding Curves

A.L. Mikheikin, Yu.D. Nechipurenko, A.S. Zasedatelev and S.A. Streltsov

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Complexing of Duplex DNA with a Pair of Pseudocomplementary PNAs

Ekaterina Protozanova, Vadim V. Demidov and Maxim D. Frank-Kamenetskii

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Computer Aided Study of Ligand Binding to with Catalytic Domain of Avian Sarcoma Virus Integrase

V.Kothekar, S. Shankar and A. Kumar

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Conditionally active ribozymes: Hammerhead-Mn-miniribozyme cassettes

Brian H. Johnston (1, 2), Tai-Chih Kuo (1), and Sergei A. Kazakov (1)

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Conformation of Azidoguanosine: An Anti-AIDS Drug

Azra Parveen and R. P. Ojha

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Conformational Dynamics of Nucleic Acids: Monte Carlo Sampling in the Space of Rigid Body and Sugar Pucker Variables

Remo Rohs and Heinz Sklenar

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Constructing DNA Based Molecular Machines

Bernard Yurke

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Crystal structure of the clamp loader small subunit from Pyrococcus furiosus

Takuji Oyama(1), Yoshizumi Ishino(2), Isaac K. O. Cann(2) and Kosuke Morikawa(1)

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Crystal Structure Of The NarL Effector Domain-DNA Complex

Ann E. Maris(1), Michael Sawaya(2), Maria Grzeskowiak(2), Mike Jarvis(3),, Mary L. Kopka(2),Robert Gunsalus(3), Richard E. Dickerson(2)

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Crystal Structure of Trbp111: a Structure-Specific tRNA Binding Protein

Manal A. Swairjo(1), Arturo J. Morales (1, 2), Chien-Chia Wanh (1), Angel R. Ortiz (3, 4), and, Paul Schimmel(1)

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Crystal structures of DNA Holliday junctions: Effects of sequence, ions, and drugs.

P. Shing Ho, Brandt F. Eichman, and Jeffrey M. Vargason,

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Deformable Elements in the Promoter DNA as a Basis for Adaptive Conformational Transitions

O. N. Ozoline (1), I. S. Masulis (1) and V. A. Buckin (2)

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Designing Effective Inhibitors of HIV-1 RT

Gye Won Han (1), Mary L. Kopka (1), J. M. Lown (2) and R. E. Dickerson (1)

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Determinants For Specificity in U1A-RNA Interaction

Felicia Pitici and David L. Beveridge

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DNA Binding Properties of Bis-linked Netropsin Derivatives with Head-to-Head and Tail-to-Tail Orientations of Two Netropsin Moieties

A.N. Surovaya (1), G. Burckhardt (2), S. L. Grokhovsky (1,3), Ch. Zimmer (2) and G. V. Gursky (1)

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DNA Binding to Cr(III) and Cr(III)-tannin Complexes Studied by FTIR Spectroscopy and Capillary Electrophoresis

H. Arakawa, N. Watanabe and H. A. Tajmir-Riahi

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DNA Condensation Studied by Vibrational Circular Dichroism (VCD) and IR Spectroscopy

V. Andrushchenko (1), J.H. van de Sande (2) and H.Wieser (1)

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DNA Damage Probed By Molecular Dynamics Simulations

Daniel Barsky

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DNA Hydrolysis Catalyzed by a HNH Endonuclease- Colicin E7 Protein

Meng-Jiun Sui (1), Wen-Yen Ku (1), Yu-Wen Liu (1, 2), Kin-Fu Chak (2) and Hanna S. Yuan (1)

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DNA mediated energy transfer from 4',6-diamidino-2-phenylindole to [Ru(1,10-phenanthroline)2L]2+: Ligand size effect

Jungho Yoon(1), Chang-Beom Cho(1), Seog K. Kim(1), and Maeng-Joon Jung(2)

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DNA-Protein Recognition in the Presence of Solvent

D. Sivanesan and W. J. Welsh

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Drug binding to the Packaging Region of HIV-1

Mark P. McPike, Jerry Goodisman and James C. Dabrowiak,

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Dynamics of Escherichia coli Fpg-protein interaction with DNA substrates

O. Fedorova (1), V. Koval (1), A. Ishchenko (1), N. Vasilenko (1), G. Nevinsky (1), K. Douglas (2)

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Dynamics of the interaction between L11 and EF-G during tRNA translocation

Joachim Frank(1,3), Rajendra Agrawal(2), Jamie Linde(2), Jayati Sengupta(2), Knud H. Nierhaus(4)

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Electron and Scanning Force Microscopy of Supercoiled DNA Molecules

Dmitry I. Cherny and Thomas M. Jovin

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Electron Transfer Through DNA-Modified Surfaces: Detection of Single Base Mismatches and Other Perturbations to the Base Stack

Elizabeth M. Boon (1), Michael G. Hill (2), and Jacqueline K. Barton (1)

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Eletron microscopic image analysis of macromolecules involved in DNA replication, repair, and recombination

Mayanagi, K. (1), Miyata, T. (1), Yamada, K.(1,2), Ariyoshi, M.(1), Cann, I.(1) Yuasa, M.(1), Ishino, Y.(1), Ohnishi, T.(2), Iwasaki, H.(2,3), Shinagawa, H.(2) and Morikawa, K.(1)

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Elucidation of the Folding Mechanism of Fis, A dimeric DNA-Binding Protein

Sarah A. Hobart(1), Sergey Ilin(1), Robert Osuna(2), and Wilfredo Colon(1)

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Energetics of the Sequence-Specific Interactions of the ETS Domain of Murine PU.1.

Gregory Man Kai Poon and Robert B. Macgregor, Jr.

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Evolution of the Triplet Code and the Earliest Proteins.

E. N. Trifonov

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Exploring the free energy landscape of a biomolecular bond

Torsten Strunz, Irina Schumakovitch, Wilfried Grange, Hans-Joachim G?ntherodt, Martin Hegner

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Fluorescence Studies of the Conformations of the N- and C-Domains of Monomeric and Octameric Saccharomyces Cerevisiae TATA Binding Protein (TBP) and Complexed With DNA.

Sergei Khrapunov and Michael Brenowitz

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Formation of Intramolecular DNA Triplex Monitored by Fluorescence of 2-aminopurine Incorporated in the Third Strand

Dmitry N. Kaluzhny (1), Olga F. Borisova (1), Robert L. Jernigan (2), Victor B. Zhurkin (2), Anna K. Shchyolkina (1)

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From Minichaperone To GroEL: A homage to Paul Sigler

A. R. Fersht, A. M. Buckle, Q. Wang, J. Chatellier, F. Hill

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Functional Complexes of the 70S Ribosome

Harry F. Noller(1), Marat M. Yusupov(1,2), Gulnara Zh. Yusupova(1,2), Albion Baucom(1), Kate Lieberman(1), Thomas N. Earnest(3), Laura Lancaster(1), Anne Dallas(1), Kurt Fredrick(1), J.H.C. Cate(4)

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Functional implications from the structure of the small ribosomal subunit in complex with edeine and the initiation factor 3 (IF3).

François Franceschi

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Global and local deformability of DNA oligonucleotides

Filip Lankas (1), Jirí Sponer (1), Pavel Hobza (1), Jörg Langowski (2)

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Global Optimization of Potential Energy to Predict Protein and Crystal Structure

H.A. Scheraga(1), J. Pillardy(1), A. Liwo(1), C. Czaplewski(1), J. Lee(1), D.R. Ripoll(2), W.J. Wedemeyer(1), and Y.A. Arnautova(1)

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High-Resolution Imaging Surface Structures with the Scanning Force Microscope (SFM): A Study on Living Cancer Cells, Fibroblasts and Chondrocytes

Gerlinde Bischoff (1), Robert Bischoff (2), Dagmar Riemann (3), Jürgen Langner (3), Hans-Joachim Hein (4),

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High-resolution NMR Structure of an AT-rich DNA Fragment Refined with the miniCarlo Program

Nikolai B. Ulyanov (1), William R. Bauer (2) and Thomas L. James (1)

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HIV-1 exploits a novel tRNA(Lys3) structure for reverse transcription

Tricia Elgavish, Lesley C. DupuyÝ, Michael L. Miller, Daniel E. Golden, Stephen L. Hajduk, Casey D. MorrowÝ, & Stephen C. Harvey

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HIV-1 Polypurine Tract RNA/DNA Decamer Crystal Structure With an Unusual Sugar Conformation

Mary L. Kopka, Gye Won Han, Laurence Lavelle, Ho Leung Ng and Richard E. Dickerson

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How the Formation of DNA Tetraplexes Turns Oncogenes On and Off

Tomas Simonsson

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HU Binding to Bent DNA: A Fluorescence Resonance Energy Transfer Study

Kristi Wojtuszewski and Ishita Mukerji;

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Human Cell Death and Aging: Denatured Single-Stranded DNA

Claude E. Gagna(1,2,), Wojciech Golebiewski(2), and W. Clark Lambert(1)

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Identification of CAP Binding Sites Using Hidden Markov Models

Kelly M. Thayer (1) and David L. Beveridge (2)

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Improved binding of pyrimidine a-DNAs with phosphoramidate linkages to their DNA targets studied by FTIR and UV spectroscopy.

Bei-Wen Sun à, Fr?d?ric Geinguenaud à, Eliane Taillandier à Magali Naval ¤, Alain Laurent ¤, Fran?oise Debart ¤, Jean-Jacques Vasseur ¤

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Increased Binding Affinity of Caffeine to Denatured DNA and its Modulatory Effect on DNA-Binding Agents Cisplatin, Novontrone, and Ethidium Bromide

R.Malathi, S. G. Bhuvan Kumar and I. Maria Johnson

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Increased resolution in NMR structure determination from experiments in dilute liquid crystalline media.

Zhengrong Wu,(1) Masatsune Kainosho,(2) Nico Tjandra,(3) and Ad Bax(1)

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Insights to subsite recognition in thiol protease inhibitor complexes: understanding specificity, the basis of differential inhibition.

Asim K. Bera, Suparna Bhattacharya, Asok K. Pal, Sawan Sen, Sibani Chakraborty, Sreya Ghosh, Soumen Ghosh, U. Halder, B.P. Mukhopadhyay and Asok Banerjee.

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Interaction of a designed interleukin-10 epitope mimic with an antibody studied by isothermal titration microcalorimetry

Karin Welfle (1), Rolf Misselwitz (1,3), Robert Sabat (2),Hans-Dieter Volk (2), , Jens Schneider-Mergener (2,4), Ulrich Reineke (2,4) and Heinz Welfle (1)

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