Publications (co-)authored by students in the Biophysics program

2017

[1] 

Bobo Shi, Yun Kyung Shin, Ali A Hassanali, and Sherwin J Singer
"Biomolecules at the amorphous silica/water interface: Binding and fluorescence anisotropy of peptides."
Colloids Surf B Biointerfaces 157, 83-92 (2017).

[2] 

Elihu C Ihms, Ian R Kleckner, Paul Gollnick, and Mark P Foster
"Mechanistic Models Fit to Variable Temperature Calorimetric Data Provide Insights into Cooperativity."
Biophys. J. 112, 1328-1338 (2017).

[3] 

Jeffrey W Slater, Sean C Marguet, Sabrina L Cirino, Pearson T Maugeri, and Hannah S Shafaat
"Experimental and DFT Investigations Reveal the Influence of the Outer Coordination Sphere on the Vibrational Spectra of Nickel-Substituted Rubredoxin, a Model Hydrogenase Enzyme."
Inorg Chem 56, 3926-3938 (2017).

[4] 

Christine Wachnowsky, Nathaniel A Wesley, Insiya Fidai, and J A Cowan
"Understanding the Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 1 MMDS1-Impact of a Disease-Causing Gly208Cys Substitution on Structure and Activity of NFU1 in the Fe/S Cluster Biosynthetic Pathway."
J. Mol. Biol. 429, 790-807 (2017).

[5] 

E John Tokarsky, Petra C Wallenmeyer, Kenneth K Phi, and Zucai Suo
"Significant impact of divalent metal ions on the fidelity, sugar selectivity, and drug incorporation efficiency of human PrimPol."
DNA Repair Amst. 49, 51-59 (2017).

[6] 

Meng Zhang, Lijuan Wang, and Dongping Zhong
"Photolyase: Dynamics and Mechanisms of Repair of Sun-Induced DNA Damage."
Photochem. Photobiol. 93, 78-92 (2017).

[7] 

Shane D Walton, Harshini Chakravarthy, Vikram Shettigar, Andrew J ONeil, Jalal K Siddiqui, Benjamin R Jones, Svetlana B Tikunova, and Jonathan P Davis
"Divergent Soybean Calmodulins Respond Similarly to Calcium Transients: Insight into Differential Target Regulation."
Front Plant Sci 8, 208 (2017).

 

2016

[1] 

Insiya Fidai, Christine Wachnowsky, and J A Cowan
"Mapping cellular Fe-S cluster uptake and exchange reactions - divergent pathways for iron-sulfur cluster delivery to human ferredoxins."
Metallomics 8, 1283-1293 (2016).

[2] 

Christine Wachnowsky, Insiya Fidai, and James A Cowan
"Cytosolic iron-sulfur cluster transfer-a proposed kinetic pathway for reconstitution of glutaredoxin 3."
FEBS Lett. 590, 4531-4540 (2016).

[3] 

Amritraj Patra, Dustin A Politica, Arindom Chatterjee, E John Tokarsky, Zucai Suo, Ashis K Basu, Michael P Stone, and Martin Egli
"Mechanism of Error-Free Bypass of the Environmental Carcinogen N-2-Deoxyguanosin-8-yl-3-aminobenzanthrone Adduct by Human DNA Polymerase η."
Chembiochem 17, 2033-2037 (2016).

[4] 

Meng Zhang, Lijuan Wang, Shi Shu, Aziz Sancar, and Dongping Zhong
"Bifurcating electron-transfer pathways in DNA photolyases determine the repair quantum yield."
Science 354, 209-213 (2016).

[5] 

Insiya Fidai, Christine Wachnowsky, and J A Cowan
"Glutathione-complexed 2Fe-2S clusters function in Fe-S cluster storage and trafficking."
J. Biol. Inorg. Chem. 21, 887-901 (2016).

[6] 

Christine Wachnowsky, Insiya Fidai, and J A Cowan
"Iron-sulfur cluster exchange reactions mediated by the human Nfu protein."
J. Biol. Inorg. Chem. 21, 825-36 (2016).

[7] 

E John Tokarsky, Varun V Gadkari, Walter J Zahurancik, Chanchal K Malik, Ashis K Basu, and Zucai Suo
"Pre-steady-state kinetic investigation of bypass of a bulky guanine lesion by human Y-family DNA polymerases."
DNA Repair Amst. 46, 20-28 (2016).

[8] 

Joshua P Ferguson, Nathan M Willy, Spencer P Heidotting, Scott D Huber, Matthew J Webber, and Comert Kural
"Deciphering dynamics of clathrin-mediated endocytosis in a living organism."
J. Cell Biol. 214, 347-58 (2016).

[9] 

Jenny V Le, Yi Luo, Michael A Darcy, Christopher R Lucas, Michelle F Goodwin, Michael G Poirier, and Carlos E Castro
"Probing Nucleosome Stability with a DNA Origami Nanocaliper."
ACS Nano 10, 7073-84 (2016).

[10] 

Jonathan P Davis, Vikram Shettigar, Svetlana B Tikunova, Sean C Little, Bin Liu, Jalal K Siddiqui, Paul M L Janssen, Mark T Ziolo, and Shane D Walton
"Designing proteins to combat disease: Cardiac troponin C as an example."
Arch. Biochem. Biophys. 601, 4-10 (2016).

[11] 

Jeffrey R Tonniges, Benjamin Albert, Edward P Calomeni, Shuvro Roy, Joan Lee, Xiaokui Mo, Susan E Cole, and Gunjan Agarwal
"Collagen Fibril Ultrastructure in Mice Lacking Discoidin Domain Receptor 1."
Microsc. Microanal. 22, 599-611 (2016).

[12] 

Michelle L Asp, Frances V Sjaastad, Jalal K Siddiqui, Jonathan P Davis, and Joseph M Metzger
"Effects of Modified Parvalbumin EF-Hand Motifs on Cardiac Myocyte Contractile Function."
Biophys. J. 110, 2094-105 (2016).

[13] 

Bobo Shi, Mithila V Agnihotri, Si-Han Chen, Richie Black, and Sherwin J Singer
"Polarization charge: Theory and applications to aqueous interfaces."
J Chem Phys 144, 164702 (2016).

[14] 

Carol J Huseby and Jeff Kuret
"Analyzing Tau Aggregation with Electron Microscopy."
Methods Mol. Biol. 1345, 101-12 (2016).

[15] 

Patrick D Halley, Christopher R Lucas, Emily M McWilliams, Matthew J Webber, Randy A Patton, Comert Kural, David M Lucas, John C Byrd, and Carlos E Castro
"DNA Origami: Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug-Resistance Mechanisms in a Leukemia Model Small 3/2016."
Small 12, 307 (2016).

[16] 

Patrick D Halley, Christopher R Lucas, Emily M McWilliams, Matthew J Webber, Randy A Patton, Comert Kural, David M Lucas, John C Byrd, and Carlos E Castro
"Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug-Resistance Mechanisms in a Leukemia Model."
Small 12, 308-20 (2016).

[17] 

Nathan D Jones, Miguel A Lopez, Jeungphill Hanne, Mitchell B Peake, Jong-Bong Lee, Richard Fishel, and Kristine E Yoder
"Retroviral intasomes search for a target DNA by 1D diffusion which rarely results in integration."
Nat Commun 7, 11409 (2016).

[18] 

Kruthika Sundaram, Mohd Akhlakur Rahman, Srabani Mitra, Daren L Knoell, Shireen A Woodiga, Samantha J King, and Mark D Wewers
"IκBζ Regulates Human Monocyte Pro-Inflammatory Responses Induced by Streptococcus pneumoniae."
PLoS ONE 11, e0161931 (2016).

[19] 

M D Gibson, M Brehove, Y Luo, J North, and M G Poirier
"Methods for Investigating DNA Accessibility with Single Nucleosomes."
Meth. Enzymol. 581, 379-415 (2016).

[20] 

Hussam E Salhi, Nathan C Hassel, Jalal K Siddiqui, Elizabeth A Brundage, Mark T Ziolo, Paul M L Janssen, Jonathan P Davis, and Brandon J Biesiadecki
"Myofilament Calcium Sensitivity: Mechanistic Insight into TnI Ser-23/24 and Ser-150 Phosphorylation Integration."
Front Physiol 7, 567 (2016).

[21] 

Jalal K Siddiqui, Svetlana B Tikunova, Shane D Walton, Bin Liu, Meredith Meyer, Pieter P de Tombe, Nathan Neilson, Peter M Kekenes-Huskey, Hussam E Salhi, Paul M L Janssen, Brandon J Biesiadecki, and Jonathan P Davis
"Myofilament Calcium Sensitivity: Consequences of the Effective Concentration of Troponin I."
Front Physiol 7, 632 (2016).

 

2015

[1] 

Jingwei Li, Stephen A Pearson, Kevin D Fenk, and J A Cowan
"Glutathione-coordinated 2Fe-2S cluster is stabilized by intramolecular salt bridges."
J. Biol. Inorg. Chem. 20, 1221-7 (2015).

[2] 

Matthew Brehove, Tao Wang, Justin North, Yi Luo, Sarah J Dreher, John C Shimko, Jennifer J Ottesen, Karolin Luger, and Michael G Poirier
"Histone Core Phosphorylation Regulates DNA Accessibility."
J. Biol. Chem. 290, 22612-21 (2015).

[3] 

Kruthika Sundaram, Srabani Mitra, Mikhail A Gavrilin, and Mark D Wewers
"House Dust Mite Allergens and the Induction of Monocyte Interleukin 1β Production That Triggers an IκBζ-Dependent Granulocyte Macrophage Colony-Stimulating Factor Release from Human Lung Epithelial Cells."
Am. J. Respir. Cell Mol. Biol. 53, 400-11 (2015).

[4] 

Bobo Shi, Yun Kyung Shin, Ali A Hassanali, and Sherwin J Singer
"DNA Binding to the Silica Surface."
J Phys Chem B 119, 11030-40 (2015).

[5] 

Jie Gao, Xu Wang, Meng Zhang, Mingdi Bian, Weixian Deng, Zecheng Zuo, Zhenming Yang, Dongping Zhong, and Chentao Lin
"Trp triad-dependent rapid photoreduction is not required for the function of Arabidopsis CRY1."
Proc. Natl. Acad. Sci. U.S.A. 112, 9135-40 (2015).

[6] 

Elihu C Ihms and Mark P Foster
"MESMER: minimal ensemble solutions to multiple experimental restraints."
Bioinformatics 31, 1951-8 (2015).

[7] 

Comert Kural, Ahmet Ata Akatay, Raphaël Gaudin, Bi-Chang Chen, Wesley R Legant, Eric Betzig, and Tom Kirchhausen
"Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edges of motile cells and on protrusions of immobile cells."
Mol. Biol. Cell 26, 2044-53 (2015).

[8] 

Rajan Vyas, Andrew J Reed, E John Tokarsky, and Zucai Suo
"Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography."
J. Am. Chem. Soc. 137, 5225-30 (2015).

[9] 

Sara N Lim, Anil K Pradhan, Rolf F Barth, Sultana N Nahar, Robin J Nakkula, Weilian Yang, Alycia M Palmer, Claudia Turro, Michael Weldon, Erica Hlavin Bell, and Xiaokui Mo
"Tumoricidal activity of low-energy 160-KV versus 6-MV X-rays against platinum-sensitized F98 glioma cells."
J. Radiat. Res. 56, 77-89 (2015).

[10] 

Kaylan M Haizlip, Nima Milani-Nejad, Lucia Brunello, Kenneth D Varian, Jessica L Slabaugh, Shane D Walton, Sandor Gyorke, Jonathan P Davis, Brandon J Biesiadecki, and Paul M L Janssen
"Dissociation of Calcium Transients and Force Development following a Change in Stimulation Frequency in Isolated Rabbit Myocardium."
Biomed Res Int 2015, 468548 (2015).

[11] 

Morgan Bernier, Yi Luo, Kingsley C Nwokelo, Michelle Goodwin, Sarah J Dreher, Pei Zhang, Mark R Parthun, Yvonne Fondufe-Mittendorf, Jennifer J Ottesen, and Michael G Poirier
"Linker histone H1 and H3K56 acetylation are antagonistic regulators of nucleosome dynamics."
Nat Commun 6, 10152 (2015).

[12] 

Dipu Mohan Kumar, Mingqun Lin, Qingming Xiong, Mathew James Webber, Comert Kural, and Yasuko Rikihisa
"EtpE Binding to DNase X Induces Ehrlichial Entry via CD147 and hnRNP-K Recruitment, Followed by Mobilization of N-WASP and Actin."
MBio 6, e01541-15 (2015).

[13] 

Sarah Hulbert and Hojjat Adeli
"Spotting psychopaths using technology."
Rev Neurosci 26, 721-32 (2015).

 

2014

[1] 

Insiya Fidai, Lalintip Hocharoen, Seth Bradford, Christine Wachnowsky, and J A Cowan
"Inactivation of sortase A mediated by metal ATCUN complexes."
J. Biol. Inorg. Chem. 19, 1327-39 (2014).

[2] 

Yi Luo, Justin A North, and Michael G Poirier
"Single molecule fluorescence methodologies for investigating transcription factor binding kinetics to nucleosomes and DNA."
Methods 70, 108-18 (2014).

[3] 

Cai Chen and Ralf Bundschuh
"Quantitative models for accelerated protein dissociation from nucleosomal DNA."
Nucleic Acids Res. 42, 9753-60 (2014).

[4] 

Hussam E Salhi, Shane D Walton, Nathan C Hassel, Elizabeth A Brundage, Pieter P de Tombe, Paul M L Janssen, Jonathan P Davis, and Brandon J Biesiadecki
"Cardiac troponin I tyrosine 26 phosphorylation decreases myofilament Ca2 sensitivity and accelerates deactivation."
J. Mol. Cell. Cardiol. 76, 257-264 (2014).

[5] 

Xiakun Chu, Fei Liu, Brian A Maxwell, Yong Wang, Zucai Suo, Haijun Wang, Wei Han, and Jin Wang
"Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA."
PLoS Comput. Biol. 10, e1003804 (2014).

[6] 

Varun V Gadkari, E John Tokarsky, Chanchal K Malik, Ashis K Basu, and Zucai Suo
"Mechanistic investigation of the bypass of a bulky aromatic DNA adduct catalyzed by a Y-family DNA polymerase."
DNA Repair Amst. 21, 65-77 (2014).

[7] 

Kristen E Funk, Stefani N Thomas, Kelsey N Schafer, Grace L Cooper, Zhongping Liao, David J Clark, Austin J Yang, and Jeff Kuret
"Lysine methylation is an endogenous post-translational modification of tau protein in human brain and a modulator of aggregation propensity."
Biochem. J. 462, 77-88 (2014).

[8] 

Cuiling Xu, Brian A Maxwell, and Zucai Suo
"Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis."
J. Mol. Biol. 426, 2901-17 (2014).

[9] 

Mithila V Agnihotri, Si-Han Chen, Corey Beck, and Sherwin J Singer
"Displacements, mean-squared displacements, and codisplacements for the calculation of nonequilibrium properties."
J Phys Chem B 118, 8170-8 (2014).

[10] 

Mu Zhang, Shengyan Xiang, Heui-Yun Joo, Lei Wang, Kendra A Williams, Wei Liu, Chen Hu, Dan Tong, Joshua Haakenson, Chuangui Wang, Shengping Zhang, Ryan E Pavlovicz, Amanda Jones, Kristina H Schmidt, Jinfu Tang, Huiqin Dong, Bin Shan, Bin Fang, Rangasudhagar Radhakrishnan, Peter M Glazer, Patrick Matthias, John Koomen, Edward Seto, Gerold Bepler, Santo V Nicosia, Jiandong Chen, Chenglong Li, Liya Gu, Guo-Min Li, Wenlong Bai, Hengbin Wang, and Xiaohong Zhang
"HDAC6 Deacetylates and Ubiquitinates MSH2 to Maintain Proper Levels of MutSα."
Mol. Cell 55, 31-46 (2014).

[11] 

Huyen T Nguyen, Kamal S Pohar, Guang Jia, Zarine K Shah, Amir Mortazavi, Debra L Zynger, Lai Wei, Daniel Clark, Xiangyu Yang, and Michael V Knopp
"Improving Bladder Cancer Imaging Using 3-T Functional Dynamic Contrast-Enhanced Magnetic Resonance Imaging."
Invest Radiol 49, 390-395 (2014).

[12] 

Seth S Bradford, Martin James Ross, Insiya Fidai, and James A Cowan
"Insight into the Recognition, Binding, and Reactivity of Catalytic Metallodrugs Targeting Stem Loop IIb of Hepatitis C IRES RNA."
ChemMedChem 9, 1275-85 (2014).

[13] 

Brian A Maxwell and Zucai Suo
"Recent insight into the kinetic mechanisms and conformational dynamics of y-family DNA polymerases."
Biochemistry 53, 2804-14 (2014).

[14] 

Brian A Maxwell, Cuiling Xu, and Zucai Suo
"Conformational Dynamics of a Y-Family DNA Polymerase during Substrate Binding and Catalysis As Revealed by Interdomain Förster Resonance Energy Transfer."
Biochemistry 53, 1768-78 (2014).

[15] 

Benjamin R Nixon, Shane D Walton, Bo Zhang, Elizabeth A Brundage, Sean C Little, Mark T Ziolo, Jonathan P Davis, and Brandon J Biesiadecki
"Combined troponin I Ser-150 and Ser-23/24 phosphorylation sustains thin filament Ca2 sensitivity and accelerates deactivation in an acidic environment."
J. Mol. Cell. Cardiol. 72, 177-185 (2014).

[16] 

Elihu C Ihms, Mowei Zhou, Yun Zhang, Ian R Kleckner, Craig A McElroy, Vicki H Wysocki, Paul Gollnick, and Mark P Foster
"Gene regulation by substoichiometric heterocomplex formation of undecameric TRAP and trimeric anti-TRAP."
Proc. Natl. Acad. Sci. U.S.A. 111, 3442-7 (2014).

[17] 

Yi Luo, Justin A North, Sean D Rose, and Michael G Poirier
"Nucleosomes accelerate transcription factor dissociation."
Nucleic Acids Res. 42, 3017-27 (2014).

[18] 

Huameng Li, Hui Xiao, Li Lin, David Jou, Vandana Kumari, Jiayuh Lin, and Chenglong Li
"Drug design targeting protein-protein interactions PPIs using multiple ligand simultaneous docking MLSD and drug repositioning: discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 interface."
J. Med. Chem. 57, 632-41 (2014).

[19] 

Wenbo Wei, Guang Jia, David Flanigan, Jinyuan Zhou, and Michael V Knopp
"Chemical exchange saturation transfer MR imaging of articular cartilage glycosaminoglycans at 3T: Accuracy of B0 Field Inhomogeneity corrections with gradient echo method."
Magn Reson Imaging 32, 41-7 (2014).

[20] 

Hsiang-Ting Ho, Bin Liu, Jedidiah S Snyder, Qing Lou, Elizabeth A Brundage, Florencia Velez-Cortes, Honglan Wang, Mark T Ziolo, Mark E Anderson, Chandan K Sen, Xander H T Wehrens, Vadim V Fedorov, Brandon J Biesiadecki, Thomas J Hund, and Sándor Györke
"Ryanodine receptor phosphorylation by oxidized CaMKII contributes to the cardiotoxic effects of cardiac glycosides."
Cardiovasc. Res. 101, 165-74 (2014).

[21] 

Jerry Curran, Lifei Tang, Steve R Roof, Sathya Velmurugan, Ashley Millard, Stephen Shonts, Honglan Wang, Demetrio Santiago, Usama Ahmad, Matthew Perryman, Donald M Bers, Peter J Mohler, Mark T Ziolo, and Thomas R Shannon
"Nitric Oxide-Dependent Activation of CaMKII Increases Diastolic Sarcoplasmic Reticulum Calcium Release in Cardiac Myocytes in Response to Adrenergic Stimulation."
PLoS ONE 9, e87495 (2014).

[22] 

Mohd Akhlakur Rahman, Kruthika Sundaram, Srabani Mitra, Mikhail A Gavrilin, and Mark D Wewers
"Receptor interacting protein-2 plays a critical role in human lung epithelial cells survival in response to fas-induced cell-death."
PLoS ONE 9, e92731 (2014).

[23] 

William C Ray, R Wolfgang Rumpf, Brandon Sullivan, Nicholas Callahan, Thomas Magliery, Raghu Machiraju, Bang Wong, Martin Krzywinski, and Christopher W Bartlett
"Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests."
BMC Proc 8, S1 (2014).

[24] 

Katryna Cisek, Grace L Cooper, Carol J Huseby, and Jeff Kuret
"Structure and mechanism of action of tau aggregation inhibitors."
Curr Alzheimer Res 11, 918-27 (2014).

 

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