Publications

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Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.
Liu Y, Prigozhin MB, Schulten K, Gruebele M. 2014. Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment. Journal of the American Chemical Society 136(11): 4265-72. DOI: 10.1021/ja412639u
Antibodies VRC01 and 10E8 neutralize HIV-1 with high breadth and potency even with Ig-framework regions substantially reverted to germline.
Georgiev IS, Rudicell RS, Saunders KO, Shi W, Kirys T, McKee K, O'Dell S, Chuang GY, Yang ZY, Ofek G, et al. 2014. Antibodies VRC01 and 10E8 neutralize HIV-1 with high breadth and potency even with Ig-framework regions substantially reverted to germline. Journal of immunology (Baltimore, Md. : 1950) 192(3): 1100-1106. DOI: 10.4049/jimmunol.1302515
Backbone flexibility of CDR3 and immune recognition of antigens.
Haidar JN, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z. 2014. Backbone flexibility of CDR3 and immune recognition of antigens. Journal of molecular biology 426(7): 1583-99. DOI: 10.1016/j.jmb.2013.12.024
A positive cooperativity binding model between Ly49 natural killer cell receptors and the viral immunoevasin m157: kinetic and thermodynamic studies.
Romasanta PN, Curto LM, Urtasun N, Sarratea MB, Chiappini S, Miranda MV, Delfino JM, Mariuzza RA, Fernández MM, Malchiodi EL. 2014. A positive cooperativity binding model between Ly49 natural killer cell receptors and the viral immunoevasin m157: kinetic and thermodynamic studies. The Journal of biological chemistry 289(8): 5083-96. DOI: 10.1074/jbc.M113.532929
Small G proteins Rac1 and Ras regulate serine/threonine protein phosphatase 5 (PP5)·extracellular signal-regulated kinase (ERK) complexes involved in the feedback regulation of Raf1.
Mazalouskas MD, Godoy-Ruiz R, Weber DJ, Zimmer DB, Honkanen RE, Wadzinski BE. 2014. Small G proteins Rac1 and Ras regulate serine/threonine protein phosphatase 5 (PP5)·extracellular signal-regulated kinase (ERK) complexes involved in the feedback regulation of Raf1. The Journal of biological chemistry 289(7): 4219-32. DOI: 10.1074/jbc.M113.518514
Reconstitution of cholesterol-dependent vaginolysin into tethered phospholipid bilayers: implications for bioanalysis.
Budvytyte R, Pleckaityte M, Zvirbliene A, Vanderah DJ, Valincius G. 2013. Reconstitution of cholesterol-dependent vaginolysin into tethered phospholipid bilayers: implications for bioanalysis. PloS one 8(12): e82536. DOI: 10.1371/journal.pone.0082536
Critical assessment of methods of protein structure prediction (CASP)--round x.
Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. 2014. Critical assessment of methods of protein structure prediction (CASP)--round x. Proteins 82 Suppl 2: 1-6. DOI: 10.1002/prot.24452
Structural basis for HIV-1 neutralization by 2F5-like antibodies m66 and m66.6.
Ofek G, Zirkle B, Yang Y, Zhu Z, McKee K, Zhang B, Chuang GY, Georgiev IS, O'Dell S, Doria-Rose N, et al. 2014. Structural basis for HIV-1 neutralization by 2F5-like antibodies m66 and m66.6. Journal of virology 88(5): 2426-41. DOI: 10.1128/JVI.02837-13
Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10.
Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, et al. 2014. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins 82 Suppl 2: 26-42. DOI: 10.1002/prot.24489
Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor.
Manvilla BA, Pozharski E, Toth EA, Drohat AC. 2013. Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor. Acta crystallographica. Section D, Biological crystallography 69(Pt 12): 2555-62. DOI: 10.1107/S0907444913027042
Using Small-Angle Scattering Techniques to Understand Mechanical Properties of Biopolymer-Based Biomaterials.
Hyland LL, Taraban MB, Yu YB. 2013. Using Small-Angle Scattering Techniques to Understand Mechanical Properties of Biopolymer-Based Biomaterials. Soft matter 9(43): . DOI: 10.1039/C3SM51209F
Structure of the S100A4/myosin-IIA complex.
Ramagopal UA, Dulyaninova NG, Varney KM, Wilder PT, Nallamsetty S, Brenowitz M, Weber DJ, Almo SC, Bresnick AR. 2013. Structure of the S100A4/myosin-IIA complex. BMC structural biology 13: 31. DOI: 10.1186/1472-6807-13-31
Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach.
Raman EP, Yu W, Lakkaraju SK, MacKerell AD. 2013. Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. Journal of chemical information and modeling 53(12): 3384-98. DOI: 10.1021/ci4005628
Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II.
Varney KM, Bonvin AM, Pazgier M, Malin J, Yu W, Ateh E, Oashi T, Lu W, Huang J, Diepeveen-de Buin M, et al. 2013. Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II. PLoS pathogens 9(11): e1003732. DOI: 10.1371/journal.ppat.1003732
Biological functionalization of drug delivery carriers to bypass size restrictions of receptor-mediated endocytosis independently from receptor targeting.
Ansar M, Serrano D, Papademetriou I, Bhowmick TK, Muro S. 2013. Biological functionalization of drug delivery carriers to bypass size restrictions of receptor-mediated endocytosis independently from receptor targeting. ACS nano 7(12): 10597-611. DOI: 10.1021/nn404719c