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Journal Club

Students and faculty in the Biophysics Group meet every other week to discuss recent developments in the biophysics literature.

The Memorial University Biophysics Society Journal Club

Week Presenter Paper
20 Christopher Rowley

Folding of Fourteen Small Proteins with a Residue-Specific Force Field and Replica-Exchange Molecular Dynamics. 

F. Jiang, Y.-D. Wu, J. Am. Chem. Soc. 2014, 136 (27), 9536–9539

DOI: 10.1021/ja502735c

19 Lucas Stewart

AFM Indentation Study of Breast Cancer Cells

Q.S. Li, G.Y.H. Lee, C.N. Ong, C.T. Lim, Biochem. Biophys. Res. Commun. 2008, 374 (3-4), 609–613

DOI: 10.1016/j.bbrc.2008.07.078

18 Collin Knight

Bicelles Exhibiting Magnetic Alignment for a Broader Range of Temperatures: A Solid-State NMR Study

Yamamoto, K.; Pearcy, P.; Ramamoorthy, A. Langmuir, 2014, 30 (6), 1622–1629

DOI: 10.1021/la404331t

17 Tadiwos Getachew Asrat

Comprehensive Evaluation of Solution Nuclear Magnetic Resonance Spectroscopy Sample Preparation for Helical Integral Membrane Proteins

Page, R., J. Moore, H. Nguyen, M. Sharma, R. Chase, F. Gao, C. Mobley, C. Sanders, L. Ma, F. Sönnichsen, S. Lee, S. Howell, S. Opella, and T. Cross. J. Struct. Func. Genom. 2006, 7, 51–64

DOI: 10.1007/s10969-006-9009-9

16 Chris Miranda

Topology and Lipid Selectivity of Pulmonary Surfactant Protein SP-B in Membranes:
Answers from Fluorescence

Cabré, E. J., Loura, L. M. S, Fedorov, A., Perez-Gil J., Prieto, M., Biochimica et Biophysica Acta, 2012, 1818, 1717–1725

DOI:10.1016/j.bbamem.2012.03.008

15 Muyi Ant Xu

Discrimination of Bladder Cancer Cells from Normal Urothelial Cells with High Specificity and Sensitivity: Combined Application of Atomic Force Microscopy and Modulated Raman Spectroscopy

Elisabetta Canetta, Andrew Riches, Eva Borger, Simon Herrington, Kishan Dholakia, Ashok K. Adya, Acta Biomaterialia

DOI: 10.1016/j.actbio.2013.12.057

14 Saleh Riahi

Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations

Marrink, S. W.,  Berendsen, H. J. C. J. Phys. Chem., 1996, 100 (41), 16729–16738

DOI: 10.1021/jp952956f

13 Mohammad Hassan

Membrane Interactions of the Amphipathic Amino Terminus of Huntingtin

Michalek, M., Salnikov, E. S., Werten, S., and Bechinger, B. Biochemistry, 2013, 52 (5), 847–858

DOI: 10.1021/bi301325q

12 Kristen Poduska

Investigation of Surfactant Mediated Acid–Base Charging of Mineral Oxide Particles Dispersed in Apolar Systems

Gacek, MM, Berg, JC. Langmuir, 2012, 28 (51), 17841–17845

DOI: 10.1021/la303943k

11 Tadiwos Getachew Asrat

Utilizing Dynamic Light Scattering as a Process Analytical Technology for Protein Folding and Aggregation Monitoring in Vaccine Manufacturing.

Yu Z, Reid JC, and Yang YP. J. Pharm. Sci. 2013, 4284-4290

DOI: 10.1002/jps.23746

10 Justin King

Proline substitution of dimer interface β-strand residues as a strategy for the design of functional monomeric proteins.

Prem Raj B. Joseph, Krishna Mohan Poluri, Pavani Gangavarapu, Lavanya Rajagopalan, Sandeep Raghuwanshi, Ricardo M. Richardson, Roberto P. Garofalo, and Krishna Rajarathnam. Biophys. J. 2013, 1491-1501

DOI: 10.1016/j.bpj.2013.08.008

9 Gagandeep Sandhu 

Proline facilitates membrane insertion of the antimicrobial peptide maculatin 1.1 via surface indentation and subsequent lipid disordering.

David I. Fernandez, Tzong-Hsien Lee, Marc-Antoine Sani, Marie-Isabel Aguilar, and Frances Separovic. Biophys. J. 2013, 1495–1507

DOI10.1016/j.bpj.2013.01.059

8 Erika Merschrod

Immobilization of chondroitin sulfate to lipid membranes and its interactions with ECM proteins

Noomi Altgärde, Jana Becher, Stephanie Möller, Franz E. Weber, Matthias Schnabelrauch, Sofia Svedhem, J. Colloid Interface Sci. 2013, 390, 258–266

DOI10.1016/j.jcis.2012.07.063

7 Christopher Rowley

Perspective On the Martini Model

Siewert J. Marrink and D. Peter Tieleman, Chem. Soc. Rev., 2013, 42, 6801

DOI: 10.1039/c3cs60093a

6 Mohammad Hassan

Design of an Acid-Activated Antimicrobial Peptide for Tumor Therapy

Jingjing Song, Wei Zhang, Ming Kai, Jianbo Chen, Ranran Liang, Xin Zheng, Guolin Li, Bangzhi Zhang, Kairong Wang, Yun Zhang, Zhibin Yang, Jingman Ni, and Rui Wang Mol. Pharmaceutics, 2013, 10 (8), 2934–2941

DOI: 10.1021/mp400052s

5 Justin King

Base-Flipping Propensities of Unmethylated, Hemimethylated, and Fully Methylated CpG Sites

Caterina Bianchi and Ronen Zangi J. Phys. Chem. B, 2013, 117 (8), 2348–2358

DOI: 10.1021/jp312145b

4 Breanne Coady

Hydrophobic Amino Acids in the Hinge Region of the 5A Apolipoprotein Mimetic Peptide are Essential for Promoting Cholesterol Efflux by the ABCA1 Transporter

Denis O. Sviridov, Alexander M. Andrianov, Ivan V. Anishchenko, John A. Stonik, Marcelo J. A. Amar, Scott Turner, Alan T. Remaley J. Pharmacol. Exp. Ther. 2013, 344, 50–58

DOI: 10.1124/jpet.112.198143

3 Mark McDonald

Canonical Azimuthal Rotations and Flanking Residues Constrain the Orientation of Transmembrane Helices

Orlando L. Sánchez-Muñoz, Erik Strandberg, E. Esteban-Martín, Stephan L. Grage, Anne S. Ulrich, Jesús Salgado, Biophys. J.  104, 1508–1516

DOI: 10.1016/j.bpj.2013.02.030

2 Valerie Booth

Imaging the action of antimicrobial peptides on living bacterial cells.

Gee, M. L., Burton, M., Grevis-James, A., Hossain, M. A., McArthur, S., Palombo, E. A., Wade, J. D., and Clayton, A. H. Sci. Rep. 2013, 3, 1557

DOI: 10.1038/srep01557

1 Jessica Besaw

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

K. A. Beauchamp, Y-S. Lin, R. Das, V.S. Pande J. Chem. Theory Comput., 2012, 8 (4), 1409–1414

DOI:10.1021/ct2007814

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