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

2019

[1] 

Carol J Huseby, Ralf Bundschuh, and Jeff Kuret
"The role of annealing and fragmentation in human tau aggregation dynamics."
J. Biol. Chem. 294, 4728-4737 (2019).

[2] 

Yanhui Ma, Elias Pavlatos, Keyton Clayson, Xueliang Pan, Sunny Kwok, Thomas Sandwisch, and Jun Liu
"Mechanical Deformation of Human Optic Nerve Head and Peripapillary Tissue in Response to Acute IOP Elevation."
Invest. Ophthalmol. Vis. Sci. 60, 913-920 (2019).

[3] 

Chao-Min Huang, Anjelica Kucinic, Jenny V Le, Carlos E Castro, and Hai-Jun Su
"Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis."
Nanoscale 11, 1647-1660 (2019).

[4] 

David A Yeung, Nirvan Shanker, Anjum Sohail, Brent A Weiss, Carolyn Wang, Jack Wellmerling, Subhadip Das, Ramesh K Ganju, Jeanette L C Miller, Andrew B Herr, Rafael Fridman, and Gunjan Agarwal
"Clustering, Spatial Distribution, and Phosphorylation of Discoidin Domain Receptors 1 and 2 in Response to Soluble Collagen I."
J. Mol. Biol. 431, 368-390 (2019).

 

2018

[1] 

A R Blissett, B Deng, P Wei, K J Walsh, B Ollander, J Sifford, A D Sauerbeck, D W McComb, D M McTigue, and G Agarwal
"Sub-cellular In-situ Characterization of Ferritiniron in a Rodent Model of Spinal Cord Injury."
Sci Rep 8, 3567 (2018).

[2] 

Grace L Cooper, Carol J Huseby, Claire N Chandler, Jean-Christophe Cocuron, Ana P Alonso, and Jeff Kuret
"A liquid chromatography tandem mass spectroscopy approach for quantification of protein methylation stoichiometry."
Anal. Biochem. 545, 72-77 (2018).

[3] 

Pearson T Maugeri, Julia J Griese, Rui M Branca, Effie K Miller, Zachary R Smith, Jürgen Eirich, Martin Högbom, and Hannah S Shafaat
"Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in a Heterobimetallic Oxidase."
J. Am. Chem. Soc. 140, 1471-1480 (2018).

[4] 

Stephanie S Kim, Justin T Seffernick, and Steffen Lindert
"Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application."
J Phys Chem B 122, 3920-3930 (2018).

[5] 

Elias Pavlatos, Yanhui Ma, Keyton Clayson, Xueliang Pan, and Jun Liu
"Regional Deformation of the Optic Nerve Head and Peripapillary Sclera During IOP Elevation."
Invest. Ophthalmol. Vis. Sci. 59, 3779-3788 (2018).

[6] 

Sheng-Wei Chang, Jack Wellmerling, Xiaoli Zhang, Rachael E Rayner, Wissam Osman, Sara Mertz, Amal O Amer, Mark E Peeples, Prosper N Boyaka, and Estelle Cormet-Boyaka
"The psychoactive substance of cannabis Δ9-tetrahydrocannabinol THC negatively regulates CFTR in airway cells."
Biochim Biophys Acta Gen Subj 1862, 1988-1994 (2018).

 

2017

[1] 

Nathaniel A Wesley, Christine Wachnowsky, Insiya Fidai, and J A Cowan
"Understanding the molecular basis for multiple mitochondrial dysfunctions syndrome 1 MMDS1: impact of a disease-causing Gly189Arg substitution on NFU1."
FEBS J. 284, 3838-3848 (2017).

[2] 

Nathaniel A Wesley, Christine Wachnowsky, Insiya Fidai, and J A Cowan
"Analysis of NFU-1 metallocofactor binding-site substitutions-impacts on iron-sulfur cluster coordination and protein structure and function."
FEBS J. 284, 3817-3837 (2017).

[3] 

Meng Zhang, Lijuan Wang, and Dongping Zhong
"Photolyase: Dynamics and electron-transfer mechanisms of DNA repair."
Arch. Biochem. Biophys. 632, 158-174 (2017).

[4] 

Martin James Ross, Insiya Fidai, and James A Cowan
"Analysis of Structure-Activity Relationships Based on the Hepatitis C Virus SLIIb Internal Ribosomal Entry Sequence RNA-Targeting GGHYRFK⋅Cu Complex."
Chembiochem 18, 1743-1754 (2017).

[5] 

Maximillian S Westphal, Sara N Lim, Sultana N Nahar, Enam Chowdhury, and Anil K Pradhan
"Broadband, monochromatic and quasi-monochromatic x-ray propagation in multi-Z media for imaging and diagnostics."
Phys Med Biol 62, 6361-6378 (2017).

[6] 

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).

[7] 

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).

[8] 

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).

[9] 

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).

[10] 

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).

[11] 

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

[12] 

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).

[13] 

Keyton Clayson, Xueliang Pan, Elias Pavlatos, Ryan Short, Hugh Morris, Richard T Hart, and Jun Liu
"Corneoscleral stiffening increases IOP spike magnitudes during rapid microvolumetric change in the eye."
Exp. Eye Res. 165, 29-34 (2017).

[14] 

Jon delEtoile and Hojjat Adeli
"Graph Theory and Brain Connectivity in Alzheimers Disease."
Neuroscientist 23, 616-626 (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).

 

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