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Volume 94(1);  January 1, 2008
New and Notable
DNA Sequence Mediates Nucleosome Structure and Stability
Shantanu Sharma and Nikolay V. Dokholyan
Biophys J. 2008 January 1; 94(1): 1–3. Published online 2007 October 12. doi: 10.1529/biophysj.107.119172.
PMCID: PMC2134875
Don't Blink: Observing the Ultra-Fast Contraction of Spasmonemes
Wallace F. Marshall
Biophys J. 2008 January 1; 94(1): 4–5. Published online 2007 October 12. doi: 10.1529/biophysj.107.118166.
PMCID: PMC2134872
Biophysical Theory and Modeling
Stretching to Understand Proteins—A Survey of the Protein Data Bank
Joanna I. Sułkowska and Marek Cieplak
Biophys J. 2008 January 1; 94(1): 6–13. Published online 2007 August 17. doi: 10.1529/biophysj.107.105973.
PMCID: PMC2134851
Molecular Basis of Phospholipase A2 Activity toward Phospholipids with sn-1 Substitutions
Lars Linderoth, Thomas L. Andresen, Kent Jørgensen, Robert Madsen, and Günther H. Peters
Biophys J. 2008 January 1; 94(1): 14–26. Published online 2007 September 7. doi: 10.1529/biophysj.107.110106.
PMCID: PMC2134884
Mechanism of Auxin Interaction with Auxin Binding Protein (ABP1): A Molecular Dynamics Simulation Study
Branimir Bertoša, Biserka Kojić-Prodić, Rebecca C. Wade, and Sanja Tomić
Biophys J. 2008 January 1; 94(1): 27–37. Published online 2007 August 31. doi: 10.1529/biophysj.107.109025.
PMCID: PMC2134879
Site-Specific Solvation of the Photoexcited Protochlorophyllide a in Methanol: Formation of the Hydrogen-Bonded Intermediate State Induced by Hydrogen-Bond Strengthening
Guang-Jiu Zhao and Ke-Li Han
Biophys J. 2008 January 1; 94(1): 38–46. Published online 2007 September 7. doi: 10.1529/biophysj.107.113738.
PMCID: PMC2134880
Apparent Directional Scanning for DNA Repair
Tong Zhao and Aaron R. Dinner
Biophys J. 2008 January 1; 94(1): 47–52. Published online 2007 September 7. doi: 10.1529/biophysj.107.110619.
PMCID: PMC2134852
Buffered Diffusion around a Spherical Proton Pumping Cell: A Theoretical Analysis
Giovanni Zifarelli, Paolo Soliani, and Michael Pusch
Biophys J. 2008 January 1; 94(1): 53–62. Published online 2007 September 7. doi: 10.1529/biophysj.107.111310.
PMCID: PMC2134849
Humidity Dependence of Charge Transport through DNA Revealed by Silicon-Based Nanotweezers Manipulation
Christophe Yamahata, Dominique Collard, Tetsuya Takekawa, Momoko Kumemura, Gen Hashiguchi, and Hiroyuki Fujita
Biophys J. 2008 January 1; 94(1): 63–70. Published online 2007 September 7. doi: 10.1529/biophysj.107.115980.
PMCID: PMC2134877
Microseconds Dynamics Simulations of the Outer-Membrane Protease T
Marilisa Neri, Marc Baaden, Vincenzo Carnevale, Claudio Anselmi, Amos Maritan, and Paolo Carloni
Biophys J. 2008 January 1; 94(1): 71–78. Published online 2007 September 7. doi: 10.1529/biophysj.107.116301.
PMCID: PMC2134885
How a Vicinal Layer of Solvent Modulates the Dynamics of Proteins
Canan Atilgan, Ayse Ozlem Aykut, and Ali Rana Atilgan
Biophys J. 2008 January 1; 94(1): 79–89. Published online 2007 September 7. doi: 10.1529/biophysj.107.116426.
PMCID: PMC2134863
Sampling the Cell with Anomalous Diffusion—The Discovery of Slowness
Gernot Guigas and Matthias Weiss
Biophys J. 2008 January 1; 94(1): 90–94. Published online 2007 September 7. doi: 10.1529/biophysj.107.117044.
PMCID: PMC2134854
Identification of High Affinity Fatty Acid Binding Sites on Human Serum Albumin by MM-PBSA Method
Shin-ichi Fujiwara and Takashi Amisaki
Biophys J. 2008 January 1; 94(1): 95–103. Published online 2007 September 7. doi: 10.1529/biophysj.107.111377.
PMCID: PMC2134860
Membranes
Phase Fluctuations on the Micron-Submicron Scale in GUVs Composed of a Binary Lipid Mixture
Anna Celli, Sabrina Beretta, and Enrico Gratton
Biophys J. 2008 January 1; 94(1): 104–116. Published online 2007 August 31. doi: 10.1529/biophysj.107.105353.
PMCID: PMC2134868
Temperature Dependence of Structure, Bending Rigidity, and Bilayer Interactions of Dioleoylphosphatidylcholine Bilayers
Jianjun Pan, Stephanie Tristram-Nagle, Norbert Kučerka, and John F. Nagle
Biophys J. 2008 January 1; 94(1): 117–124. Published online 2007 September 7. doi: 10.1529/biophysj.107.115691.
PMCID: PMC2134881
Role of GAP-43 in Sequestering Phosphatidylinositol 4,5-Bisphosphate to Raft Bilayers
Jihong Tong, Lam Nguyen, Adriana Vidal, Sidney A. Simon, J. H. Pate Skene, and Thomas J. McIntosh
Biophys J. 2008 January 1; 94(1): 125–133. Published online 2007 September 7. doi: 10.1529/biophysj.107.110536.
PMCID: PMC2134862
Nucleic Acids
Aggregation and Adsorption at the Air-Water Interface of Bacteriophage [var phi]X174 Single-Stranded DNA
C. Douarche, J.-L. Sikorav, and A. Goldar
Biophys J. 2008 January 1; 94(1): 134–146. Published online 2007 August 31. doi: 10.1529/biophysj.107.107771.
PMCID: PMC2134866
Sequence-Dependent Variations Associated with H2A/H2B Depletion of Nucleosomes
L. Kelbauskas, N. Chan, R. Bash, P. DeBartolo, J. Sun, N. Woodbury, and D. Lohr
Biophys J. 2008 January 1; 94(1): 147–158. Published online 2007 October 12. doi: 10.1529/biophysj.107.111906.
PMCID: PMC2134853
Portal Motor Velocity and Internal Force Resisting Viral DNA Packaging in Bacteriophage [var phi]29
John Peter Rickgauer, Derek N. Fuller, Shelley Grimes, Paul J. Jardine, Dwight L. Anderson, and Douglas E. Smith
Biophys J. 2008 January 1; 94(1): 159–167. Published online 2007 September 7. doi: 10.1529/biophysj.107.104612.
PMCID: PMC2134861
Photobiophysics
Singlet Oxygen Photosensitization by EGFP and its Chromophore HBDI
Ana Jiménez-Banzo, Santi Nonell, Johan Hofkens, and Cristina Flors
Biophys J. 2008 January 1; 94(1): 168–172. Published online 2007 August 31. doi: 10.1529/biophysj.107.107128.
PMCID: PMC2134865
Proteins
Solution Structure of Poly(ethylene) Glycol-Conjugated Hemoglobin Revealed by Small-Angle X-Ray Scattering: Implications for a New Oxygen Therapeutic
Dmitri I. Svergun, Fredrik Ekström, Kim D. Vandegriff, Ashok Malavalli, Dale A. Baker, Calle Nilsson, and Robert M. Winslow
Biophys J. 2008 January 1; 94(1): 173–181. Published online 2007 September 7. doi: 10.1529/biophysj.107.114314.
PMCID: PMC2134876
Experimental Parameterization of an Energy Function for the Simulation of Unfolded Proteins
Anders B. Norgaard, Jesper Ferkinghoff-Borg, and Kresten Lindorff-Larsen
Biophys J. 2008 January 1; 94(1): 182–192. Published online 2007 September 7. doi: 10.1529/biophysj.107.108241.
PMCID: PMC2134871
Low Resolution Structural Models of the Basic Helix-Loop-Helix Leucine Zipper Domain of Upstream Stimulatory Factor 1 and Its Complexes with DNA from Small Angle X-Ray Scattering Data
Ekaterina P. Lamber, Matthias Wilmanns, and Dmitri I. Svergun
Biophys J. 2008 January 1; 94(1): 193–197. Published online 2007 September 7. doi: 10.1529/biophysj.107.112243.
PMCID: PMC2134867
Supramolecular Assemblies
Interactions of Hydrophobin Proteins in Solution Studied by Small-Angle X-Ray Scattering
Kaisa Kisko, Géza R. Szilvay, Ulla Vainio, Markus B. Linder, and Ritva Serimaa
Biophys J. 2008 January 1; 94(1): 198–206. Published online 2007 September 7. doi: 10.1529/biophysj.107.112359.
PMCID: PMC2134873
Spectroscopy, Imaging, Other Techniques
High Resolution Traction Force Microscopy Based on Experimental and Computational Advances
Benedikt Sabass, Margaret L. Gardel, Clare M. Waterman, and Ulrich S. Schwarz
Biophys J. 2008 January 1; 94(1): 207–220. Published online 2007 September 7. doi: 10.1529/biophysj.107.113670.
PMCID: PMC2134850
Supercritical Angle Fluorescence Correlation Spectroscopy
Jonas Ries, Thomas Ruckstuhl, Dorinel Verdes, and Petra Schwille
Biophys J. 2008 January 1; 94(1): 221–229. Published online 2007 September 7. doi: 10.1529/biophysj.107.115998.
PMCID: PMC2134864
Exploring Transferrin-Receptor Interactions at the Single-Molecule Level
Alexandre Yersin, Toshiya Osada, and Atsushi Ikai
Biophys J. 2008 January 1; 94(1): 230–240. Published online 2007 September 14. doi: 10.1529/biophysj.107.114637.
PMCID: PMC2134874
Helix Conformations in 7TM Membrane Proteins Determined Using Oriented-Sample Solid-State NMR with Multiple Residue-Specific 15N Labeling
Thomas Vosegaard, Miya Kamihira-Ishijima, Anthony Watts, and Niels Chr. Nielsen
Biophys J. 2008 January 1; 94(1): 241–250. Published online 2007 September 7. doi: 10.1529/biophysj.107.116004.
PMCID: PMC2134869
Cell Biophysics
Cell Shape Dynamics in Escherichia coli
Galina Reshes, Sharon Vanounou, Itzhak Fishov, and Mario Feingold
Biophys J. 2008 January 1; 94(1): 251–264. Published online 2007 August 31. doi: 10.1529/biophysj.107.104398.
PMCID: PMC2134870
Power-Limited Contraction Dynamics of Vorticella convallaria: An Ultrafast Biological Spring
A. Upadhyaya, M. Baraban, J. Wong, P. Matsudaira, A. van Oudenaarden, and L. Mahadevan
Biophys J. 2008 January 1; 94(1): 265–272. Published online 2007 October 12. doi: 10.1529/biophysj.107.108852.
PMCID: PMC2134882
Endothelial Cell Migration on RGD-Peptide-Containing PEG Hydrogels in the Presence of Sphingosine 1-Phosphate
Bradley K. Wacker, Shannon K. Alford, Evan A. Scott, Meghna Das Thakur, Gregory D. Longmore, and Donald L. Elbert
Biophys J. 2008 January 1; 94(1): 273–285. Published online 2007 September 7. doi: 10.1529/biophysj.107.109074.
PMCID: PMC2134859
The C-Terminal Transmembrane Domain of Bcl-xL Mediates Changes in Mitochondrial Morphology
Jing-Yi Zheng, Yien-Che Tsai, Pradeep Kadimcherla, Rong Zhang, Julia Shi, George A. Oyler, and Nada N. Boustany
Biophys J. 2008 January 1; 94(1): 286–297. Published online 2007 August 31. doi: 10.1529/biophysj.107.104323.
PMCID: PMC2134878
The Forces Applied by Cilia Depend Linearly on Their Frequency Due to Constant Geometry of the Effective Stroke
Zvi Teff, Zvi Priel, and Levi A. Gheber
Biophys J. 2008 January 1; 94(1): 298–305. Published online 2007 September 14. doi: 10.1529/biophysj.107.111724.
PMCID: PMC2134883
A Comparison of Step-Detection Methods: How Well Can You Do?
Brian C. Carter, Michael Vershinin, and Steven P. Gross
Biophys J. 2008 January 1; 94(1): 306–319. Published online 2007 September 7. doi: 10.1529/biophysj.107.110601.
PMCID: PMC2134886
Directly Monitoring Individual Retrovirus Budding Events Using Atomic Force Microscopy
Micha Gladnikoff and Itay Rousso
Biophys J. 2008 January 1; 94(1): 320–326. Published online 2007 September 7. doi: 10.1529/biophysj.107.114579.
PMCID: PMC2134855
Comments to the Editor
Response to Bianco et al.: Interaction Forces between F-actin and Titin PEVK Domain Measured with Optical Tweezers
Kenneth S. Campbell and Martin Lakie
Biophys J. 2008 January 1; 94(1): 327–328. Published online 2007 October 5. doi: 10.1529/biophysj.107.114322.
PMCID: PMC2134857
Muscle Thixotropy: More than Just Cross-Bridges? Response to Comment by Campbell and Lakie
Miklós S. Z. Kellermayer, Pasquale Bianco, Zsolt Mártonfalvi, Attila Nagy, András Kengyel, Dávid Szatmári, Tamás Huber, Marco Linari, Marco Caremani, and Vincenzo Lombardi
Biophys J. 2008 January 1; 94(1): 329–330. Published online 2007 October 5. doi: 10.1529/biophysj.107.122309.
PMCID: PMC2134856
Biophysical Letters
The Bacillus subtilis RNA Helicase YxiN is Distended in Solution
Shuying Wang, Michael T. Overgaard, YaoXiong Hu, and David B. McKay
Biophys J. 2008 January 1; 94(1): L01–L03. Published online 2007 October 19. doi: 10.1529/biophysj.107.120709.
PMCID: PMC2134858
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