Structural Biology / Molecular Biophysics Student Publications

Lv, C., Aitchison, E. W., Wu, D., Zheng, L., Cheng, X., & Yang, W. (2015). Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling. Journal of computational chemistry.

H. Ke, Z. Zhang, and O. Steinbock, “Scroll waves pinned to moving heterogeneities”, Phys. Rev. E 91, 032930, 1-5, 2015.

H. Ke, Z. Zhang, and O. Steinbock, “Scroll wave drift along steps, troughs and corners”, Chaos, 2015 (Submitted).

H. Ke, Z. Zhang, and O. Steinbock, “Pinned chemical waves in the presence of Stokes flow”, J. Phys. Chem. A 118, 6819-6826, 2014.

Mykhailo Kopylov, Hank W. Bass, M. Elizabeth Stroupe. The Maize (Zea maysL.)Nucleoside Diphosphate Kinase1 (ZmNDPK1)Gene Encodes a Human NM23-H2 Homologue That Binds and Stabilizes G-Quadruplex DNA. Biochemistry, 2015; 54 (9): 1743 DOI: 10.1021/bi501284g

A Single Aromatic Core Mutation Converts a Designed “Primitive” Protein from Halophile to Mesophile Folding, Longo, L.M., Tenorio, C.A., Kumru, O.S., Middaugh, C.R. and Blaber, M. Protein Science (in press) (2014)

McGee LW, Aitchison EW, Caudle SB, Morrison AJ, Zheng L, et al. (2014) Payoffs, Not Tradeoffs, in the Adaptation of a Virus to Ostensibly Conflicting Selective Pressures. PLoS Genet 10(10): e1004611. doi: 10.1371/journal.pgen.1004611

Hariri H, Bhattacharya N, Johnson K, Noble AJ, Stagg SM. Insights into the Mechanisms of Membrane Curvature and Vesicle Scission by the Small GTPase Sar1 in the Early Secretory Pathway. J Mol Biol. 2014 Sep 1.

Mutation Choice to Eliminate Buried Free Cysteines in Protein Therapeutics, Xia, X., Longo, L.M. and Blaber, M. J. Pharm. Sci. (2014 )

Detergent optimized membrane protein reconstitution in liposomes for solid state NMR. Murray DT, Griffin J, Cross TA. Biochemistry. 2014 Apr 22;53(15):2454-63. doi: 10.1021/bi500144h. Epub 2014 Apr 9.

Membrane protein structural validation by oriented sample solid-state NMR: diacylglycerol kinase. Murray DT, Li C, Gao FP, Qin H, Cross TA. Biophys J. 2014 Apr 15;106(8):1559-69. doi: 10.1016/j.bpj.2014.02.026.

Evolution and Design of Protein Structure by Folding Nucleus Symmetric Expansion, Longo, L.M., Kumru, O.S., Middaugh, C.R. and Blaber, M.  Cell: Structure (2014)

Solid State NMR: The Essential Technology for Helical Membrane Protein Structural Characterization. Timothy Cross, Vindana Ekanayake, Joana Paulino, Anna Wright. Journal of Magnetic Resonance (Impact Factor: 2.32). 01/2013; DOI: 10.1016/j.jmr.2013.12.006

G Marshall A, T Blakney G, Chen T, K Kaiser N, M McKenna A, P Rodgers R, M Ruddy B, Xian F. Mass resolution and mass accuracy: how much is enough?”Mass Spectrom (Tokyo). 2013; 2 (Spec Iss): S0009. 10.5702/massspectrometry.S0009

Jiménez ZA, Zhang Z, Steinbock O.  “Electric-field-controlled unpinning of scroll waves.” Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov;88(5):052918. Epub 2013 Nov 27. PMID: 24329342

Noble AJ1, Zhang Q, O’Donnell J, Hariri H, Bhattacharya N, Marshall AG, Stagg SM. “A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry.”  Nat Struct Mol Biol. 2013 Feb;20(2):167-73. 

Longo, L.M. and Blaber, M., “Prebiotic Protein Design Supports a Halophile Origin of Foldable Proteins” ,Frontiers in Extreme Microbiology (2013)

Longo, L.M., Şanlı-Mohamed, G. and Blaber, M., “Biophysical Characterization of a Thermoalkalophilic Esterase from Geobacillus sp”.Journal of Proteins and Proteomics  (2013)

Longo, L.M., Lee, J., Tenorio, C.A. and Blaber, M. “Alternative Folding Nuclei Definitions Facilitate the Evolution of a Symmetric Protein Fold from a Smaller Peptide Motif”, Cell: Structure 21, 1-9 (2013) PMID: 24139990

Murray, D.T., Das, N. and Cross, T.A. “Solid State NMR Strategy for Characterizing Native Membrane Protein Structures”, Accts. Chem. Res., DOI: 10.1021/ar3003442 (2013)

Loong C., Kataoka A., Badr M.,Rogers J, Chase P.B. “Slowed Dynamics of Thin Filament Regulatory Units Reduces Ca2+ Sensitivity of Cardiac Biomechanical Function” Cellular and Molecular Bioengineering, January 2013

Loong CK*, Badr MA*, Chase PB. “Tropomyosin flexural rigidity and single Ca2+ regulatory unit dynamics: implications for cooperative regulation of cardiac muscle contraction and cardiomyocyte hypertrophy”Front Physiol. 2012;3:80. Epub 2012 Apr 4. (*equal contribution)

Bingol, K.; Salinas, R. K.; Brüschweiler, R. J. Phys. Chem. Lett. 2010, 1, 1086-1089. Higher-Rank Correlation NMR Spectra with Spectral Moment Filtering.

Bingol, K.; Brüschweiler, R. Anal. Chem. 2011, 83, 7412-7417. Deconvolution of chemical mixtures with high complexity by NMR consensus trace clustering.

Bingol, K.; Zhang, F.; Bruschweiler-Li, L.; Brüschweiler, R. J. Am. Chem. Soc. 2012, 134, 9006-9011. Carbon backbone topology of the metabolome of a cell.

Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H. Structure of the Cmr2 subunit of the CRISPR-Cas RNA silencing complex. Structure. 2012 Mar 7;20(3):545-53. PubMed PMID: 22405013.

N. Das, D.T. Murray, H. Qin, and T. A. Cross, “Lipid Bilayer Preparations of Helical Membrane Proteins for Oriented and Magic Angle Spinning Solid State NMR Samples” Nature Protocols, (2013) (In press).

P. Plocinski, N. Arora, K. Sarva, E. Blaszczyk, H. Qin, N. Das, R. Plocinska, M. Ziolkiewicz, J. Dziadek, M. Kiran, P. Gorla, T.A. Cross, M. Madiraju and M. Rajagopalan,“Mycobacterium tuberculosis CwsA interacts with CrgA and Wag31 and the CrgA-CwsA complex is involved in peptidoglycan synthesis and cell shape determination” , Journal of Bacteriology 194, 6398-6409, doi:10.1128/jb.01005-12 (2012)

Longo, L., Lee, J. and Blaber, M., Simplified Protein Design Biased for Pre-Biotic Amino Acids Yields a Foldable, Halophilic Protein,(2012) Proc. Natl. Acad. Sci. U S A. [Epub ahead of print] (2013) PMID: 23341608

Longo, L.M. and Blaber, M., Protein Design — A Vast Unexploited Resource Journal of Proteins and Proteomics 3, 78-83 (2012)

Longo, L., Lee, J. and Blaber, M., Experimental Support for the Foldability-Function Tradeoff Hypothesis: Segregation of the Folding Nucleus and Functional Regions in FGF-1 Protein Science 21, 1911-1920 (2012) PMID: 23047594

Longo, L.M. and Blaber, M. Protein Design at the Interface of the Pre-Biotic and Biotic Worlds; Archives of Biochemistry & Biophysics 526, 16-21 (2012) PMID: 22772066

Blaber, M., Lee, J. and Longo, L., Emergence of Symmetric Protein Architecture from a Simple Peptide Motif: Evolutionary Models; Cellular and Molecular Life Sciences 69, 3999-4006 (2012) PMID: 22790181

Jasbir S. Dalal, Stanley M. Stevens, Sophie Alvarez, Nathalie Munoz, Karen E. Kempler, Andrea C. Dose, Beth Burnside, Barbara-Anne Battelle. “Mouse class III myosins: kinase activity and phosphorylation sites” .Journal of Neurochemistry, 19 (4). 772-784. 2011.

Murray, D.T., Lu. Y., Cross, T.A., and Quine, J.R., Geometry of kinked protein helices from NMR data, J. Magn. Reson., 210:82-89 (2011).

Myriam Cotten, Riqiang Fu, Eric D. Gordon, Elaina L. Daza, Anna S. Kozlova, Daniel J. Hibbard, Mallorie M. Taylor, Jeffrey J. Ditto, Milton Truong, High-Resolution Structure of Piscidin in Aligned Lipid Bilayers: Implications for Antimicrobial Mode of Action, Biophysical Journal, Volume 96, Issue 3.

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HongLi - CopyMOB Graduate Program Director
Dr. Hong Li
Professor of Chemistry & Biochemistry

For more information contact:
MOB Graduate Program Coordinator