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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
33 Tadiwos Getachew Asrat

Interaction of Lung Surfactant Proteins with Anionic Phospholipids

D. Y. Takamoto, M. M. Lipp, A. von Nahmen, Ka Yee C. Lee, A. J. Waring, and J. A. Zasadzinski, Biophys. J. 2001, 81, 153–169

DOI: 10.1016/S0006-3495(01)75688-3

32 Chris Miranda

Smooth Functional Transition along a Mutational Pathway with an Abrupt Protein Fold Switch

Christian Holzgräfe and Stefan Wallin Biophys. J. (2014) 107, 1217–1225

DOI: 10.1016/j.bpj.2014.07.020

31 Dr. Andrew Smith MD, MEng

Guest Speaker

Assistant Professor, Discipline of Emergency Medicine
Cross-appointed, Faculty of Engineering and Applied Sciences

 30 Lucas Stewart

Biosensing Enhancement Using Passive Mixing Structures for Microarray-based Sensors

N. Scott Lynn Jr., José-Israel Martínez-López, Markéta Bocková, Pavel Adam, Victor Coello, Héctor R. Siller, JiÅ™í Homola Biosensors and Bioelectronics 54 (2014) 506–514


29 Gagandeep Sandhu

High-Resolution Structures and Orientations of Antimicrobial Peptides Piscidin 1 and Piscidin 3 in Fluid Bilayers Reveal Tilting, Kinking, and Bilayer Immersion

B. Scott Perrin, Jr.,Ye Tian, Riqiang Fu, Christopher V. Grant, Eduard Y. Chekmenev,
William E. Wieczorek, Alexander E. Dao, Robert M. Hayden, Caitlin M. Burzynski,
Richard M. Venable, Mukesh Sharma, Stanley J. Opella, Richard W. Pastor, and Myriam L. Cotten J. Am. Chem. Soc. 2014, 136, 3491−3504

DOI: 10.1021/ja411119m

28 Ernest Awoonor-Williams 

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

Mats H. M. Olsson, Chresten R. Søndergaard, Michal Rostkowski, and Jan H. Jensen, J. Chem. Theory Comput., 2011, 7 (2), 525–537

DOI: 10.1021/ct100578z

27 Mohammad H. Khatami

Solid-state NMR and molecular dynamics simulations reveal the oligomeric ion-channels of TM2-GABAA stabilized by intermolecular hydrogen bonding

Senthil K. Kandasamya, Dong-Kuk Leeb, Ravi P.R. Nangab, Jiadi Xub, Jose S. Santosb, Ronald G. Larsona, Ayyalusamy Ramamoorthy, Biochimica et Biophysica Acta 2009, 1788, 686–695

DOI: 10.1016/j.bbamem.2008.11.009

26 Asia Alhasawi and Dong Zhe

Size Influences the Effect of Hydrophobic Nanoparticles on Lung Surfactant Model Systems

Mridula V. Dwivedi, Rakesh Kumar Harishchandra, Olga Koshkina, Michael Maskos, and Hans-Joachim Galla, Biophys. J. 2014, 106 289–298

DOI: 10.1016/j.bpj.2013.10.036

25 Jessica Besaw

A Partially Folded Structure of Amyloid-Beta(1-40) in an Aqueous Environment

Subramanian Vivekanandan, Jeffrey R. Brender, Shirley Y. Lee, and Ayyalusamy Ramamoorthy Biochem. Biophys. Res. Commun. 2011, 411(2), 312–316.


24 Gagandeep Sandhu

Peptide:lipid ratio and membrane surface charge determine the mechanismof action of the antimicrobial peptide BP100. Conformational and functional studies

Mariana C. Manzini, Katia R. Perez, Karin A. Riske , José C. Bozelli Jr., Talita L. Santos, Marcia A. da Silva, Greice K.V. Saraiva, Mario J. Politi, Ana P. Valente, Fábio C.L. Almeida, Hernan Chaimovich, Magali A. Rodrigues, Marcelo P. Bemquerer, Shirley Schreier, Iolanda M. Cuccovia, Biochimica et Biophysica Acta 1838 (2014) 1985–1999

DOI: 10.1016/j.bbamem.2014.04.004

23 Tadiwos Getachew Asrat

Determination of the Molecular Mass and Dimensions of Membrane Proteins by Size Exclusion Chromatography

Edmund, R.S. Kunji, Harding, M., Butler, P.J.G. Akamine, P. Methods. 2008 46 (2), 62–72

DOI: 10.1016/j.ymeth.2008.10.020

22 Nury Santisteban

Membrane Curvature Modulation of Protein Activity Determined by NMR

Epand, R.M., D'Souza K., Berno, B., Schlame, M. Biochim. Biophys. Acta, 2014, in press

DOI: 10.1016/j.bbamem.2014.05.004

21 Wael Demian

Revealing the glycation sites in synthetic neoglycoconjugates formed by conjugation of the antigenic monosaccharide hapten of Vibrio cholerae O1, serotype Ogawa with the BSA protein carrier using LC-ESI-QqTOF-MS/MS

Jahouh, F., Saksena, R., Kováč, P. and Banoub, J.  J. Mass Spectrom., 2012 (47), 890–900

DOI: 10.1002/jms.2974

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


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


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


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