Dynamics of Nucleic Acids Analyzed from Base Pair Geometry
|
|
|
- Annabel Greene
- 5 years ago
- Views:
Transcription
1 Dynamics of Nucleic Acids Analyzed from Base Pair Geometry Dhananjay Bhattacharyya Biophysics Division Saha Institute of Nuclear Physics Kolkata , INDIA
2 Definition and Nomenclature of Base Pair Doublet Parameters
3 Dickerson Dodecamer (DD) d(cgcgaattcgcg) 2
4 CURVES calculated values
5 Dynamics of B-DNA on the Microsecond Time Scale Alberto Pe rez,f. Javier Luque and Modesto Orozco (2007) From X3DNA ε ζ, Indicator of BI or BII conformations α γ /ja CCC: $37.00 xxxx American Chemical Society
6 Deformation Energy Color code: blue, CpG; green, d(gpa); black, d(gpc); gray, d(apa); red, d(apt) steps. In average, one of the 10 central base pairs is opened (two H-bond distances greater than 4.5) every 7.3 ns (indicating an average time for individual base pair opening of around 70 ns). Opening of G-C base pairs is mediated by Na+ binding through Major groove and is in-plane motion Opening of A-T base pairs take place through increasing propeller twist, hence out-of-plane motion.
7 4ns MD simulation of d(cgcgcgcgcgcg) 2 and chemical modifications with PME by CHARMM. We analyzed trajectory by NUPARM
8 S replaces O in backbone of substituted DNA. It yields two chiral conformers of DNA PSR and PSS.
9
10 Comparison of (a) Sugar-pucker Pseudorotation Phase angle and (b) percentage of B II Conformation in three simulations Sugar Pucker B I -B II as measured from ε ζ
11
12 PS-R PS-S PS-S Normal PO PS-R
13 PS-S Regular Phosphate PS-R
14
15 Effect of neighboring residues on structure of d(ca).d(tg) and d(aa).d(tt) doublets MD Simulations of following sequences with Na + ions and water layer d(cgcgccaaagcg) d(cgcgccacagcg) d(cgcgccagagcg) d(cgcgccatagcg) d(cgcgacaaagcg) Analysis of X-ray crystal structures of oligonucleotides indicated drastically different types of structures of d(ca).d(tg) when flanked by different base pairs. d(cgcgaaatcgcg) d(cgcggaaacgcg) d(cgcggaagcgcg) d(cgcggaaccgcg) etc.
16 Simulation setup: DNA dodecamer, 22 Na + ions and a bag of water molecules
17
18 Base Pair Orientation Parameters of DNA from simulation and X-ray Roll of d(aa).d(tt) dinuelcotide steps Twist of d(ca).d(tg) dinucleotide steps
19 Simulation of d(cgcgaaaacgcg). d(cgcgttttcgcg) With identical setup but different random no. seed Bandyopadhyay and Bhattacharyya (2000) J. Biomol. Struct. Dynam. 18, Bandyopadhyay and Bhattacharyya (2002) J. Biomol. Struct. Dynam. 19,
20 Similarity Index: n ex = (min (f, f ') / 1000 ) *100% i i i = 1 d(aa).d(tt) steps are rigid while d(ca).d(tg) are flexible, and structure this step depends on neighboring base pairs also.
21 Cross-strand bifurcated hydrogen bonds between successive base pairs impose structural rigidity to d(aa).d(tt) doublets
22 37 DNA double helices of sequences of the form: 5 d(g-d-abcd-abcd-abcd-g)3 GG G A C T G GGGG GGGA GGGC GGGT A AGGG AGGA AGGC AGGT C CGGG CGGA CGGC CGGT T TGGG TGGA TGGC TGGT AA G A C T G GAAG GAAA GAAC GAAT A AAAG AAAA AAAC AAAT C CAAG CAAA CAAC CAAT T TAAG TAAA TAAC TAAT GA G A C T G GGAG GGAA GGAC GGAT A AGAG AGAA AGAC AGAT C CGAG CGAA CGAC CGAT T TGAG TGAA TGAC TGAT
23
24 No effect of neighboring base pairs is found on d(ca).d(tg) steps by ABCD
25 Non Canonical Base Pairs in RNA U:U WWC, freq. 671 G:A SHT, freq A:U HWT, freq. 1906
26 Representative structure of RNA double helix containing Non-Watson-Crick base pair: 2066:2072 and 2209:2215 of 1J5A.pdb
27 PDB ID Length of double helix Type of noncanonical base pair No. of noncanonical base pairs Sequence of the RNA stretch 1J5A 7 1 G U C U G G C U:U W:WC C G G U U C G 1FJG 8 A:G W:WC 1 C G C C A U G G G C G G G G U C 1N32 9 A:A S:HT A:U H:WT A:G H:ST 2AW4 11 G:A S:HT A:G H:ST 3 G C A A A C C G G U G A U G G G C C 2 G U G G G A G C A C G C G U C A G U G U G C
28 Typical simulation box (60x40x40) Å 3 for helix taken from 1N32.pdb containing 9173 atoms, including Na + ions and water G C A A A C C G G U G A U G G G C C
29 First base pair Double helical fragment from1j5a of sequence G U C U G G C C G G U U C G Last base pair Central U:U base pair
30 BP 1 G:C BP 4 Shear BP 5 G:U BP 2 U:G BP 3 G:G BP 6 G:C BP 7 G:G
31 9 base pair long RNA Fragment from 1N32 A:A s:h T A:G H:S T A:U H:W T
32 Analysis of RNA fragment from 1N32.pdb with three non-canonical base pairs Open Shear Stretch 1 st base pair 2 nd base pair Last base pair
33 Open of nine base base pairs of 1N32 fragment
34 Shear of 1N32 fragment
35 Dr. Debashree Bandyopadhyay Shayantani Mukherjee Somdutta Saha Thank You
Likelihood-Based Phylogenetic Inference
Likelihood-Based Phylogenetic Inference John P. Huelsenbeck (UC Berkeley) #NEXUS begin data; dimensions ntax=5 nchar=895; format gap=- datatype=dna; matrix Human AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGACTT...AACCCAAACAACCCAGCTCTCCCTAAGCTT
Extended description of the rigid base model (Supplement to Section 2.1: Model)
Supplementary material for cgdna: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA by D. Petkevičiūtė, M. Pasi, O. Gonzalez and J.H. Maddocks S Extended
The wonderful world of NUCLEIC ACID NMR!
Lecture 12 M230 Feigon Sequential resonance assignments in DNA (and RNA): homonuclear method 2 structure determination Reading resources Evans Chap 9 The wonderful world of NUCLEIC ACID NMR! Catalytically
NUCLEIC ACIDS. Basic terms and notions. Presentation by Eva Fadrná adapted by Radovan Fiala
UCLEIC ACIDS Basic terms and notions Presentation by Eva Fadrná adapted by Radovan Fiala RA vs DA Single strand A-RA B-DA duplex Length of A Total length of DA in a human cell 1 m (1000 km) DA in typical
In silico detection of trna sequence features characteristic to aminoacyl-trna synthetase class membership
Nucleic Acids Research Advance Access published August 17, 2007 Nucleic Acids Research, 2007, 1 17 doi:10.1093/nar/gkm598 In silico detection of trna sequence features characteristic to aminoacyl-trna
Crystal Structures of the Two Isomorphous A-DNA Decamers d(gtacgcgtac) and d(ggccgcggcc)
568 Bull. Korean Chem. Soc. 2006, Vol. 27, No. 4 Taegyun Kim et al. Crystal Structures of the Two Isomorphous A-DNA Decamers d(gtacgcgtac) and d(ggccgcggcc) Taegyun Kim, Taek Hun Kwon, Hyesun Jung, Ja
Species Tree Inference using SVDquartets
Species Tree Inference using SVDquartets Laura Kubatko and Dave Swofford May 19, 2015 Laura Kubatko SVDquartets May 19, 2015 1 / 11 SVDquartets In this tutorial, we ll discuss several different data types:
DNA Structure. Voet & Voet: Chapter 29 Pages Slide 1
DNA Structure Voet & Voet: Chapter 29 Pages 1107-1122 Slide 1 Review The four DNA bases and their atom names The four common -D-ribose conformations All B-DNA ribose adopt the C2' endo conformation All
Indian Institute of Science, Bangalore, India California Institute of Technology, Pasadena, CA 91125
Date of Submission: Email: maiti@physics.iisc.ernet.in Date of Acceptance: Understanding DNA based Nanostructures Prabal K. Maiti 1+, Tod A.Pascal 2, Nagarajan Vaidehi 2,3, and William A. Goddard III 2,
Assessing the current state of AMBER force field modifications for DNA.
Assessing the current state of AMBER force field modifications for DNA. Supporting Information. Table S1 Average structural parameters for the DDD system with the ε/ζ OL1 +χ OL4 force field modification.
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Resonance assignment and NMR spectra for hairpin and duplex A 6 constructs. (a) 2D HSQC spectra of hairpin construct (hp-a 6 -RNA) with labeled assignments. (b) 2D HSQC or SOFAST-HMQC
Supplementary Figures. Measuring Similarity Between Dynamic Ensembles of Biomolecules
Supplementary Figures Measuring Similarity Between Dynamic Ensembles of Biomolecules Shan Yang, Loïc Salmon 2, and Hashim M. Al-Hashimi 3*. Department of Chemistry, University of Michigan, Ann Arbor, MI,
Lesson Overview The Structure of DNA
12.2 THINK ABOUT IT The DNA molecule must somehow specify how to assemble proteins, which are needed to regulate the various functions of each cell. What kind of structure could serve this purpose without
Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013
Hydration of protein-rna recognition sites Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India 1 st November, 2013 Central Dogma of life DNA
Time-dependence of key H-bond/electrostatic interaction distances in the sirna5-hago2 complexes... Page S14
Supporting Information Probing the Binding Interactions between Chemically Modified sirnas and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations S. Harikrishna* and P. I. Pradeepkumar*
Describing RNA Structure by Libraries of Clustered Nucleotide Doublets
doi:10.1016/j.jmb.2005.06.024 J. Mol. Biol. (2005) 351, 26 38 Describing RNA Structure by Libraries of Clustered Nucleotide Doublets Michael T. Sykes* and Michael Levitt Department of Structural Biology,
Hydrogen and hydration of DNA and RNA oligonucleotides
Biophysical Chemistry 95 (2002) 273 282 Hydrogen and hydration of DNA and RNA oligonucleotides Muttaiya Sundaralingam*, Baocheng Pan Biological Macromolecular Structure Center, Departments of Chemistry,
Supporting information for: Role of N7 protonation of guanine in determining structure, stability and function of RNA base pairs
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2015 Supporting information for: Role of N7 protonation of guanine in determining structure,
Imaging Nucleic Acids with the AFM. W Travis Johnson PhD Agilent Technologies Nanomeasurements Division
Imaging Nucleic Acids with the AFM W Travis Johnson PhD Agilent Technologies Nanomeasurements Division Structure of DNA A T G C Standard Watson-Crick A-T & G-C base pairs in B-DNA DNA double helix composed
Chapter 9 DNA recognition by eukaryotic transcription factors
Chapter 9 DNA recognition by eukaryotic transcription factors TRANSCRIPTION 101 Eukaryotic RNA polymerases RNA polymerase RNA polymerase I RNA polymerase II RNA polymerase III RNA polymerase IV Function
Supplementary Information. The Solution Structural Ensembles of RNA Kink-turn Motifs and Their Protein Complexes
Supplementary Information The Solution Structural Ensembles of RNA Kink-turn Motifs and Their Protein Complexes Xuesong Shi, a Lin Huang, b David M. J. Lilley, b Pehr B. Harbury a,c and Daniel Herschlag
NMR of Nucleic Acids. K.V.R. Chary Workshop on NMR and it s applications in Biological Systems November 26, 2009
MR of ucleic Acids K.V.R. Chary chary@tifr.res.in Workshop on MR and it s applications in Biological Systems TIFR ovember 26, 2009 ucleic Acids are Polymers of ucleotides Each nucleotide consists of a
Hydration of Nucleotides Thomas Wyttenbach, Dengfeng Liu, and Michael T. Bowers
http://bowers.chem.ucsb.edu/ ydration of ucleotides Thomas Wyttenbach, Dengfeng Liu, and Michael T. Bowers ASMS 2006 Why study hydration? Is a certain property of a molecule (e.g. conformation) inherent
Atomic-Level Simulations of Seeman DNA Nanostructures: The Paranemic Crossover in Salt Solution
Biophysical Journal Volume 90 March 2006 1463 1479 1463 Atomic-Level Simulations of Seeman DNA Nanostructures: The Paranemic Crossover in Salt Solution Prabal K. Maiti,* y Tod A. Pascal,* Nagarajan Vaidehi,*
The ideal fiber pattern exhibits 4-quadrant symmetry. In the ideal pattern the fiber axis is called the meridian, the perpendicular direction is
Fiber diffraction is a method used to determine the structural information of a molecule by using scattering data from X-rays. Rosalind Franklin used this technique in discovering structural information
Introduction to" Protein Structure
Introduction to" Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Learning Objectives Outline the basic levels of protein structure.
Visualizing single-stranded nucleic acids in solution
1 SUPPLEMENTARY INFORMATION Visualizing single-stranded nucleic acids in solution Alex Plumridge 1, +, Steve P. Meisburger 2, + and Lois Pollack 1, * 1 School of Applied and Engineering Physics, Cornell
BIOINFORMATICS. Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths
BIOINFORMATICS Vol. 6 no. 2 Pages 865 889 Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths Pierre Baldi, 2, and Pierre-François Baisnée Department of Information
SUPPLEMENTARY INFORMATION
Supplementary Results DNA binding property of the SRA domain was examined by an electrophoresis mobility shift assay (EMSA) using synthesized 12-bp oligonucleotide duplexes containing unmodified, hemi-methylated,
Atomic-resolution Crystal Structures of B-DNA Reveal Specific Influences of Divalent Metal Ions on Conformation and Packing
Article No. jmbi.1999.2934 available online at http://www.idealibrary.com on J. Mol. Biol. (1999) 291, 83±99 Atomic-resolution Crystal Structures of B-DNA Reveal Specific Influences of Divalent Metal Ions
Introduction to Polymer Physics
Introduction to Polymer Physics Enrico Carlon, KU Leuven, Belgium February-May, 2016 Enrico Carlon, KU Leuven, Belgium Introduction to Polymer Physics February-May, 2016 1 / 28 Polymers in Chemistry and
Explicit Ion, Implicit Water Solvation for Molecular Dynamics of Nucleic Acids and Highly Charged Molecules
Explicit Ion, Implicit Water Solvation for Molecular Dynamics of Nucleic Acids and Highly Charged Molecules NINAD V. PRABHU, 1 MANORANJAN PANDA, 2 QINGYI YANG, 3 KIM A. SHARP 3 1 Schering-Plough, Kenilworth,
Divalent cations serve critical functions across a multitude of
DNA-dependent divalent cation binding in the nucleosome core particle Curt A. Davey and Timothy J. Richmond* Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg,
DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids
Biophysical Journal Volume 84 March 2003 1421 1449 1421 DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids Swarnalatha Y. Reddy,* Fabrice Leclerc,* yz and Martin Karplus* z *Department of
Supporting Information for. DNA elasticity from short DNA to nucleosomal DNA
Supporting Information for DNA elasticity from short DNA to nucleosomal DNA Ashok Garai, 1 Suman Saurabh, 1 Yves Lansac, 2 and Prabal K. Maiti* 1 1 Centre for Condensed Matter Theory, Department of Physics,
SUPPLEMENTAL MATERIAL
SUPPLEMENTAL MATERIAL Systematic Coarse-Grained Modeling of Complexation between Small Interfering RNA and Polycations Zonghui Wei 1 and Erik Luijten 1,2,3,4,a) 1 Graduate Program in Applied Physics, Northwestern
Protein Dynamics. The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron.
Protein Dynamics The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron. Below is myoglobin hydrated with 350 water molecules. Only a small
Predicting RNA structures: the model of the RNA element binding Rev meets the NMR structure Fabrice Leclerc, Jayashree Srinivasan and Robert Cedergren
Research Paper 141 Predicting RNA structures: the model of the RNA element binding Rev meets the NMR structure Fabrice Leclerc, Jayashree Srinivasan and Robert edergren Background: How accurate are the
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
volume 16 Number 6 1988 Nucleic Acids Research The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(cgcgaattcgcg) Mai-kun Teng, Nassim Usman, Christin A.Frederick and Andrew
98 Algorithms in Bioinformatics I, WS 06, ZBIT, D. Huson, December 6, 2006
98 Algorithms in Bioinformatics I, WS 06, ZBIT, D. Huson, December 6, 2006 8.3.1 Simple energy minimization Maximizing the number of base pairs as described above does not lead to good structure predictions.
Comparative Dynamics and Sequence Dependence of DNA and. RNA Binding to Single Walled Carbon Nanotubes
Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes Markita P. Landry, 1 Lela Vuković, 2,3 Sebastian Kruss, 1 Gili Bisker, 1 Alexandra M. Landry, 4 Shahrin
Investigation of dsdna Stretching Meso-Mechanics Using LS-DYNA
8 th International LS-DYNA Users Conference Simulation echnology (3) Investigation of dsdna Stretching Meso-Mechanics Using LS-DYNA C. A. Yuan and K. N. Chiang Department of Power Mechanical Engineering,
SANDRO BOTTARO, PAVEL BANÁŠ, JIŘÍ ŠPONER, AND GIOVANNI BUSSI
FREE ENERGY LANDSCAPE OF GAGA AND UUCG RNA TETRALOOPS. SANDRO BOTTARO, PAVEL BANÁŠ, JIŘÍ ŠPONER, AND GIOVANNI BUSSI Contents 1. Supplementary Text 1 2 Sample PLUMED input file. 2. Supplementary Figure
DNA bending induced during Molecular Dynamics simulations: Basepair Kinks and Hinges
DNA bending induced during Molecular Dynamics simulations: Basepair Kinks and Hinges Thursday, October 23, 2008 Theoretical Approaches or the Genome LAPTH-LAMA-LAPP-CNRS-University o Savoie Jeremy Curuksu
Spectroscopic and Molecular Dynamics Evidence for a Sequential Mechanisms for the A-to-B Transition in DNA
Wesleyan University WesScholar Division III Faculty Publications Natural Sciences and Mathematics 7-2008 Spectroscopic and Molecular Dynamics Evidence for a Sequential Mechanisms for the A-to-B Transition
Berg Tymoczko Stryer Biochemistry Sixth Edition Chapter 1:
Berg Tymoczko Stryer Biochemistry Sixth Edition Chapter 1: Biochemistry: An Evolving Science Tips on note taking... Remember copies of my lectures are available on my webpage If you forget to print them
DNA/RNA Structure Prediction
C E N T R E F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U Master Course DNA/Protein Structurefunction Analysis and Prediction Lecture 12 DNA/RNA Structure Prediction Epigenectics Epigenomics:
Advanced Cell Biology. Lecture 7
Advanced Cell Biology. Lecture 7 Alexey Shipunov Minot State University January 25, 2013 Shipunov (MSU) Advanced Cell Biology. Lecture 7 January 25, 2013 1 / 43 Outline Questions and answers Structure
Modeling Biological Systems Opportunities for Computer Scientists
Modeling Biological Systems Opportunities for Computer Scientists Filip Jagodzinski RBO Tutorial Series 25 June 2007 Computer Science Robotics & Biology Laboratory Protein: πρώτα, "prota, of Primary Importance
A nucleotide-level coarse-grained model of RNA
A nucleotide-level coarse-grained model of RNA Petr Šulc, Flavio Romano, Thomas E. Ouldridge, Jonathan P. K. Doye, and Ard A. Louis Citation: The Journal of Chemical Physics 140, 235102 (2014); doi: 10.1063/1.4881424
Effects of intra base-pairs flexibility on hole transfer coupling in DNA
Chemical Physics Letters 429 (2006) 546 550 www.elsevier.com/locate/cplett Effects of intra base-pairs flexibility on hole transfer coupling in DNA Anna Sadowska-Aleksiejew a, Janusz Rak a, *, Alexander
Why Proteins Fold? (Parts of this presentation are based on work of Ashok Kolaskar) CS490B: Introduction to Bioinformatics Mar.
Why Proteins Fold? (Parts of this presentation are based on work of Ashok Kolaskar) CS490B: Introduction to Bioinformatics Mar. 25, 2002 Molecular Dynamics: Introduction At physiological conditions, the
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
3836 J. Chem. Theory Comput. 2010, 6, 3836 3849 Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins Pavel Banáš,, Daniel Hollas, Marie Zgarbová, Petr
Gas-Phase DNA Helix Conformations
Gas-Phase DNA Helix Conformations Erin Shammel Baker, Jennifer Gidden, Alessandra Ferzoco, Thomas Wyttenbach and Michael Bowers utline Experimental Method Theoretical Method Instrumentation DNA Background
A conserved P-loop anchor limits the structural dynamics that mediate. nucleotide dissociation in EF-Tu.
Supplemental Material for A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu. Evan Mercier 1,2, Dylan Girodat 1, and Hans-Joachim Wieden 1 * 1 Alberta
SUPPLEMENTARY FIGURES
SUPPLEMENTARY FIGURES Supplementary Figure 1 Protein sequence alignment of Vibrionaceae with either a 40-residue insertion or a 44-residue insertion. Identical residues are indicated by red background.
Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rrna-l25 Protein Complex
Bowling Green State University ScholarWorks@BGSU Chemistry Faculty Publications Chemistry 11-2004 Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rrna-l25 Protein Complex Neocles
Biophysics Lectures Three and Four
Biophysics Lectures Three and Four Kevin Cahill cahill@unm.edu http://dna.phys.unm.edu/ 1 The Atoms and Molecules of Life Cells are mostly made from the most abundant chemical elements, H, C, O, N, Ca,
Structural and Engergetic Properties of Hydrogen Bonds in PNA=DNA and PNA-PNA Base Pairs: a Theoretical Study
KKU Res J. 2011; 16(6) 587 KKU Res J. 2011; 16(6): 587-595 http://resjournal.kku.ac.th Structural and Engergetic Properties of Hydrogen Bonds in PNA=DNA and PNA-PNA Base Pairs: a Theoretical Study Watcharaporn
Potential Energy (hyper)surface
The Molecular Dynamics Method Thermal motion of a lipid bilayer Water permeation through channels Selective sugar transport Potential Energy (hyper)surface What is Force? Energy U(x) F = " d dx U(x) Conformation
Analyzing the Flexibility of RNA Structures by Constraint Counting
4202 Biophysical Journal Volume 94 June 2008 4202 4219 Analyzing the Flexibility of RNA Structures by Constraint Counting Simone Fulle and Holger Gohlke Department of Biological Sciences, Molecular Bioinformatics
Nucleic Acids NMR Spectroscopy. Markus W. Germann Departments of Chemistry and Biology Georgia State University
2012 ucleic Acids MR Spectroscopy Markus W. Germann Departments of Chemistry and Biology Georgia State University Sometimes a picture helps! o animals were hurt!! MR of ucleic Acids 1! 1) MR Spectroscopy
NIH Public Access Author Manuscript Phys Rev Lett. Author manuscript; available in PMC 2013 April 16.
NIH Public Access Author Manuscript Published in final edited form as: Phys Rev Lett. 2013 March 1; 110(9): 098101. Mean-field interactions between nucleic-acid-base dipoles can drive the formation of
Table 1. Crystallographic data collection, phasing and refinement statistics. Native Hg soaked Mn soaked 1 Mn soaked 2
Table 1. Crystallographic data collection, phasing and refinement statistics Native Hg soaked Mn soaked 1 Mn soaked 2 Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell
Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6
Supplementary Information for: Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6 Yawei Dai 1, 2, Markus Seeger 3, Jingwei Weng 4, Song Song 1, 2, Wenning Wang 4, Yan-Wen 1, 2,
Base Motif Recognition and Design of DNA Templates for Fluorescent Silver Clusters by Machine Learning **
DOI: 10.1002/adma.xxxxxxxxx Base Motif Recognition and Design of DNA Templates for Fluorescent Silver Clusters by Machine Learning ** By Stacy M. Copp 1, Petko Bogdanov 2, Mark Debord 1, Ambuj Singh 2,3,
Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions
382 Biophysical Journal Volume 83 July 2002 382 406 Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions Lihua Wang,* Brian E. Hingerty, A. R. Srinivasan, Wilma
Supplementary Figure S1. Urea-mediated buffering mechanism of H. pylori. Gastric urea is funneled to a cytoplasmic urease that is presumably attached
Supplementary Figure S1. Urea-mediated buffering mechanism of H. pylori. Gastric urea is funneled to a cytoplasmic urease that is presumably attached to HpUreI. Urea hydrolysis products 2NH 3 and 1CO 2
A rigid-base model for DNA structure prediction. O. Gonzalez
A rigid-base model for DNA structure prediction O. Gonzalez Introduction Objective. To develop a model to predict the structure and flexibility of standard, B-form DNA from its sequence. Introduction Objective.
Villa et al. (2005) Structural dynamics of the lac repressor-dna complex revealed by a multiscale simulation. PNAS 102:
Villa et al. (2005) Structural dynamics of the lac repressor-dna complex revealed by a multiscale simulation. PNAS 102: 6783-6788. Background: The lac operon is a cluster of genes in the E. coli genome
Helical Structure and Circular Dichroism Spectra of DNA: A Theoretical Study
pubs.acs.org/jpca Helical Structure and Circular Dichroism Spectra of DNA: A Theoretical Study Tomoo Miyahara, Hiroshi Nakatsuji,*, and Hiroshi Sugiyama Quantum Chemistry Research Institute, JST, CREST,
Lecture 12. DNA/RNA Structure Prediction. Epigenectics Epigenomics: Gene Expression
C N F O N G A V B O N F O M A C S V U Master Course DNA/Protein Structurefunction Analysis and Prediction Lecture 12 DNA/NA Structure Prediction pigenectics pigenomics: Gene xpression ranscription factors
NOTES - Ch. 16 (part 1): DNA Discovery and Structure
NOTES - Ch. 16 (part 1): DNA Discovery and Structure By the late 1940 s scientists knew that chromosomes carry hereditary material & they consist of DNA and protein. (Recall Morgan s fruit fly research!)
Nature Structural & Molecular Biology: doi: /nsmb
Supplementary Table 1 Mean inclination angles a of wild-type and mutant K10 RNAs Base pair K10-wt K10-au-up K10-2gc-up K10-2gc-low K10-A-low 1-44 2.8 ± 0.7 4.8 ± 0.8 3.2 ± 0.6 4.3 ± 1.9 12.5 ± 0.4 2 43-2.5
Non-deterministic self-assembly with asymmetric interactions
Non-deterministic sel-assembly with asymmetric interactions S. Tesoro, K. Göprich, T. Kartanas, U. F. Keyser, and S. E. Ahnert Cavendish Laboratory, University o Cambridge, JJ Thomson Avenue, CB3 HE Cambridge,
Supplementary Data DSSR: an integrated software tool for dissecting the spatial structure of RNA by Lu et al.
Supplementary Data DSSR: an integrated software tool for dissecting the spatial structure of RNA by Lu et al. Supplementary Figures S1 The four base triplets and associated hydrogen bonds detected by DSSR
Supplemental Material
Supplemental Material Protocol S1 The PromPredict algorithm considers the average free energy over a 100nt window and compares it with the the average free energy over a downstream 100nt window separated
Retinal Proteins (Rhodopsins) Vision, Bioenergetics, Phototaxis. Bacteriorhodopsin s Photocycle. Bacteriorhodopsin s Photocycle
Molecular chanisms of Photoactivation and Spectral Tuning in Retinal Proteins Emad Tajkhorshid Theoretical and Computational Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign
Zwitterionic i-motif structures are preserved in DNA negatively charged ions. produced by electrospray mass spectrometry
S1 Zwitterionic i-motif structures are preserved in DNA negatively charged ions produced by electrospray mass spectrometry Frederic Rosu 1*, Valérie Gabelica 1, Laure Joly 1, Gilles Grégoire 2, Edwin De
Overview & Applications. T. Lezon Hands-on Workshop in Computational Biophysics Pittsburgh Supercomputing Center 04 June, 2015
Overview & Applications T. Lezon Hands-on Workshop in Computational Biophysics Pittsburgh Supercomputing Center 4 June, 215 Simulations still take time Bakan et al. Bioinformatics 211. Coarse-grained Elastic
Sugars, such as glucose or fructose are the basic building blocks of more complex carbohydrates. Which of the following
Name: Score: / Quiz 2 on Lectures 3 &4 Part 1 Sugars, such as glucose or fructose are the basic building blocks of more complex carbohydrates. Which of the following foods is not a significant source of
Assignment A08: Semi-empirical Methods (SEM) and Layer Methods (LM)
Assignment A08: Semi-empirical Methods (SEM) and Layer Methods (LM) Many reactions occur in highly anisotropic environments, which are persistent over time. This is very different from the effects of solvation,
Sodium and Chlorine Ions as Part of the DNA Solvation Shell
Biophysical Journal Volume 77 October 1999 1769 1781 1769 Sodium and Chlorine Ions as Part of the DNA Solvation Shell Michael Feig and B. Montgomery Pettitt Department of Chemistry and Institute for Molecular
Interdisciplinary Nanoscience Center University of Aarhus, Denmark. Design and Imaging. Assistant Professor.
Interdisciplinary Nanoscience Center University of Aarhus, Denmark Design and Imaging DNA Nanostructures Assistant Professor Wael Mamdouh wael@inano.dk Molecular Self-assembly Synthesis, SPM microscopy,
Combinatorial approaches to RNA folding Part I: Basics
Combinatorial approaches to RNA folding Part I: Basics Matthew Macauley Department of Mathematical Sciences Clemson University http://www.math.clemson.edu/~macaule/ Math 4500, Spring 2015 M. Macauley (Clemson)
The transformation from B-DNA in fibers (1) to dehydrated
A crystallographic map of the transition from B-DNA to A-DNA Jeffrey M. Vargason*, Keith Henderson, and P. Shing Ho* *Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis,
Supporting Information
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2016 Supporting Information Lipid molecules can induce an opening of membrane-facing
Supporting Information
Supporting Information Energies and 2 -hydroxyl group orientations of RNA backbone conformations. Benchmark CCSD(T)/CBS database, electronic analysis and assessment of DFT methods and MD simulations Arnošt
NMR parameters intensity chemical shift coupling constants 1D 1 H spectra of nucleic acids and proteins
Lecture #2 M230 NMR parameters intensity chemical shift coupling constants Juli Feigon 1D 1 H spectra of nucleic acids and proteins NMR Parameters A. Intensity (area) 1D NMR spectrum: integrated intensity
Basics of protein structure
Today: 1. Projects a. Requirements: i. Critical review of one paper ii. At least one computational result b. Noon, Dec. 3 rd written report and oral presentation are due; submit via email to bphys101@fas.harvard.edu
Supporting Information
S1 Supporting Information Unraveling the Reaction Mechanism of Enzymatic C5-Cytosine Methylation of DNA. A Combined Molecular Dynamics and QM/MM Study of Wild Type and Gln119 Variant Juan Aranda 1, Kirill
Exploring the Sequence Dependent Structure and Dynamics of DNA with Molecular Dynamics Simulation
Exploring the Sequence Dependent Structure and Dynamics of DNA with Molecular Dynamics Simulation Sarah Harris School of Physics and Astronomy University of Leeds Introduction Calculations of the charge
MOLECULAR DYNAMICS OF RNA STRUCTURAL MOTIF. TEMPERATURE ENHANCED SAMPLING OF THE CONFORMATIONAL SPACE
COMPUTATIONAL METHODS IN SCIENCE AND TECHNOLOGY 8(2), 37-45 (2002) MOLECULAR DYNAMICS OF RNA STRUCTURAL MOTIF. TEMPERATURE ENHANCED SAMPLING OF THE CONFORMATIONAL SPACE TADEUSZ KULIŃSKI, KATARZYNA KULIŃSKA
1. (5) Draw a diagram of an isomeric molecule to demonstrate a structural, geometric, and an enantiomer organization.
Organic Chemistry Assignment Score. Name Sec.. Date. Working by yourself or in a group, answer the following questions about the Organic Chemistry material. This assignment is worth 35 points with the
The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from Its Structure in Crystals of 50S Ribosomal Subunits,
11776 Biochemistry 2006, 45, 11776-11789 The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from Its Structure in Crystals of 50S Ribosomal Subunits, Neelaabh Shankar, Scott D. Kennedy,
Ramachandran and his Map
Ramachandran and his Map C Ramakrishnan Introduction C Ramakrishnan, retired professor from Molecular Biophysics Unit, Indian Institute of Science, Bangalore, has been associated with Professor G N Ramachandran
A Computational Study of Nucleosomal DNA Flexibility
Biophysical Journal Volume 91 December 2006 4121 4132 4121 A Computational Study of Nucleosomal DNA Flexibility Jory Z. Ruscio* and Alexey Onufriev y *Genetics, Bioinformatics & Computational Biology Program,
1) NMR is a method of chemical analysis. (Who uses NMR in this way?) 2) NMR is used as a method for medical imaging. (called MRI )
Uses of NMR: 1) NMR is a method of chemical analysis. (Who uses NMR in this way?) 2) NMR is used as a method for medical imaging. (called MRI ) 3) NMR is used as a method for determining of protein, DNA,
Computational Modeling of Protein Kinase A and Comparison with Nuclear Magnetic Resonance Data
Computational Modeling of Protein Kinase A and Comparison with Nuclear Magnetic Resonance Data ABSTRACT Keyword Lei Shi 1 Advisor: Gianluigi Veglia 1,2 Department of Chemistry 1, & Biochemistry, Molecular
DACH-Platinum-DNA Interactions: An Investigation into the Basis for. Binding and Recognition by parallel molecular modelling
DACH-Platinum-DNA Interactions: An Investigation into the Basis for Binding and Recognition by parallel molecular modelling Yang lifeng 1,2, Ding Jeak Ling 1 1 Department of Biological Sciences, National