Volume 96, Issue 2, Pages L7-L9 (January 2009)

Slides:



Advertisements
Similar presentations
Lever-Arm Mechanics of Processive Myosins Yujie Sun, Yale E. Goldman Biophysical Journal Volume 101, Issue 1, Pages 1-11 (July 2011) DOI: /j.bpj
Advertisements

Michael A. Geeves, Sherwin S. Lehrer  Biophysical Journal 
Maryam Sayadi, Seiichiro Tanizaki, Michael Feig  Biophysical Journal 
Dejun Lin, Alan Grossfield  Biophysical Journal 
Shaogui Wu, Laicai Li, Quan Li  Biophysical Journal 
Olivier Fisette, Stéphane Gagné, Patrick Lagüe  Biophysical Journal 
Steered Molecular Dynamics Studies of Titin I1 Domain Unfolding
Jing Han, Kristyna Pluhackova, Tsjerk A. Wassenaar, Rainer A. Böckmann 
Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer  Yu-Shan Lin, Gregory R. Bowman, Kyle A.
Christopher Wostenberg, W.G. Noid, Scott A. Showalter 
Composition Fluctuations in Lipid Bilayers
Supriyo Bhattacharya, Nagarajan Vaidehi  Biophysical Journal 
Robert P. Rambo, John A. Tainer  Biophysical Journal 
Volume 111, Issue 4, Pages (August 2016)
What Color is it?.
Liqun Zhang, Susmita Borthakur, Matthias Buck  Biophysical Journal 
Monika Sharma, Alexander V. Predeus, Nicholas Kovacs, Michael Feig 
Volume 108, Issue 1, Pages (January 2015)
Mechanism of the αβ Conformational Change in F1-ATPase after ATP Hydrolysis: Free- Energy Simulations  Yuko Ito, Mitsunori Ikeguchi  Biophysical Journal 
Anton Arkhipov, Wouter H. Roos, Gijs J.L. Wuite, Klaus Schulten 
Influence of Protein Scaffold on Side-Chain Transfer Free Energies
Blind Test of Physics-Based Prediction of Protein Structures
Volume 98, Issue 2, Pages (January 2010)
Brittny C. Davis, Jodian A. Brown, Ian F. Thorpe  Biophysical Journal 
Molecular Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop
Riboswitches: Fold and Function
Volume 113, Issue 4, Pages (August 2017)
“DFG-Flip” in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop  Harish Vashisth, Luca Maragliano, Cameron F.
SAXS-Oriented Ensemble Refinement of Flexible Biomolecules
Volume 108, Issue 7, Pages (April 2015)
Nucleotide Effects on the Structure and Dynamics of Actin
Li Sun, Jeffrey K. Noel, Herbert Levine, José N. Onuchic 
Comparative Molecular Dynamics Simulation Studies of Protegrin-1 Monomer and Dimer in Two Different Lipid Bilayers  Huan Rui, Jinhyuk Lee, Wonpil Im 
Hisashi Ishida, Hidetoshi Kono  Biophysical Journal 
Volume 18, Issue 7, Pages (July 2010)
Pek Ieong, Rommie E. Amaro, Wilfred W. Li  Biophysical Journal 
Volume 107, Issue 5, Pages (September 2014)
Replica Exchange Molecular Dynamics Simulations Provide Insight into Substrate Recognition by Small Heat Shock Proteins  Sunita Patel, Elizabeth Vierling,
Rita Pancsa, Daniele Raimondi, Elisa Cilia, Wim F. Vranken 
Volume 107, Issue 9, Pages (November 2014)
Volume 110, Issue 1, Pages (January 2016)
Velocity-Dependent Mechanical Unfolding of Bacteriorhodopsin Is Governed by a Dynamic Interaction Network  Christian Kappel, Helmut Grubmüller  Biophysical.
Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL
Volume 112, Issue 9, Pages (May 2017)
Chi H. Mak, Tyler Matossian, Wen-Yeuan Chung  Biophysical Journal 
Hierarchical Cascades of Instability Govern the Mechanics of Coiled Coils: Helix Unfolding Precedes Coil Unzipping  Elham Hamed, Sinan Keten  Biophysical.
Volume 111, Issue 4, Pages (August 2016)
Volume 114, Issue 1, Pages (January 2018)
Volume 107, Issue 7, Pages (October 2014)
Flow-Induced β-Hairpin Folding of the Glycoprotein Ibα β-Switch
Coupling of S4 Helix Translocation and S6 Gating Analyzed by Molecular-Dynamics Simulations of Mutated Kv Channels  Manami Nishizawa, Kazuhisa Nishizawa 
Coupling of S4 Helix Translocation and S6 Gating Analyzed by Molecular-Dynamics Simulations of Mutated Kv Channels  Manami Nishizawa, Kazuhisa Nishizawa 
Christina Bergonzo, Thomas E. Cheatham  Biophysical Journal 
Volume 111, Issue 11, Pages (December 2016)
Volume 98, Issue 10, Pages (May 2010)
Eric R. May, Jun Feng, Charles L. Brooks  Biophysical Journal 
Modelling Toehold-Mediated RNA Strand Displacement
Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes  Yu-ming M. Huang, Wei Chen, Michael J.
Xiaodong Pang, Huan-Xiang Zhou  Biophysical Journal 
Cardiolipin Interactions with Proteins
Interactions of the Auxilin-1 PTEN-like Domain with Model Membranes Result in Nanoclustering of Phosphatidyl Inositol Phosphates  Antreas C. Kalli, Gareth.
Volume 7, Issue 2, Pages R19-R23 (February 1999)
Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations  Takao Yoda, Yuji Sugita, Yuko Okamoto  Biophysical.
Volume 98, Issue 2, Pages (January 2010)
Amir Marcovitz, Yaakov Levy  Biophysical Journal 
Thomas Kampourakis, Yin-Biao Sun, Malcolm Irving  Biophysical Journal 
Atomic Level Rendering of DNA-Drug Encounter
Volume 112, Issue 6, Pages (March 2017)
Seongwon Kim, Takako Takeda, Dmitri K. Klimov  Biophysical Journal 
The NorM MATE Transporter from N
Presentation transcript:

Volume 96, Issue 2, Pages L7-L9 (January 2009) Nonlocal Helix Formation Is Key to Understanding S-Adenosylmethionine-1 Riboswitch Function  Paul C. Whitford, Alexander Schug, John Saunders, Scott P. Hennelly, José N. Onuchic, Kevin Y. Sanbonmatsu  Biophysical Journal  Volume 96, Issue 2, Pages L7-L9 (January 2009) DOI: 10.1016/j.bpj.2008.10.033 Copyright © 2009 Biophysical Society Terms and Conditions

Figure 1 (a) Secondary and (b) tertiary structure (PDB entry: 2GIS) of the SAM-I riboswitch. Average secondary structure formation as a function of the fraction of native contacts formed (Q; see the Supporting Material) for the (c) SAM-free and (d) SAM-present simulations. (a–d) Color scheme: P1, cyan; P2, red; P3, green; P4, blue; PK, orange; and SAM, purple in panels b and d. In panel a, SAM-contacting residues are highlighted by brown boxes. The most notable difference in folding mechanism is earlier initial folding of P1 (black arrows) at the expense of the PK (starred) when SAM is present. The folding free-energy profiles for the (e) SAM-free and (f) SAM-present simulations are shown for several temperatures (with temperature indicated by color). The most significant free-energy barrier in both systems is associated with initial P1 folding. When SAM is present, the free-energy barrier is reduced and encountered earlier in the folding process. Biophysical Journal 2009 96, L7-L9DOI: (10.1016/j.bpj.2008.10.033) Copyright © 2009 Biophysical Society Terms and Conditions

Figure 2 (a) Average percent of SAM-aptamer domain interactions formed by region as a function of the fraction of native SAM-aptamer domain contacts formed QSAM. Simulation images illustrating the SAM binding mechanism: (b) SAM binds a preformed P3 helix; (c) SAM recruits 3′ strand of P1; (d) SAM binds 5′ strand of P1; and P1 helix formation proceeds. Biophysical Journal 2009 96, L7-L9DOI: (10.1016/j.bpj.2008.10.033) Copyright © 2009 Biophysical Society Terms and Conditions