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Browsing Biochemistry and Molecular Biophysics Faculty Research and Publications by Title

Browsing Biochemistry and Molecular Biophysics Faculty Research and Publications by Title

Now showing items 1-20 of 57

Accelerate sampling in atomistic energy landscapes using topology-based coarse-grained models

Zhang, Weihong; Chen, Jianhan (2014-12-03)

We describe a multiscale enhanced sampling (MSES) method where efficient topology-based coarse-grained models are coupled with all-atom ones to enhance the sampling of atomistic protein energy landscape. The bias from the ...
ADAM12-L is a direct target of the miR-29 and miR-200 families in breast cancer

Duhachek-Muggy, S.; Zolkiewska, Anna (2015-03-04)

ADAM12-L and ADAM12-S represent two major splice variants of human metalloproteinase-disintegrin 12 mRNA, which differ in their 3'-untranslated regions (3' UTRs). ADAM12-L, but not ADAM12-S, has prognostic and chemopredictive ...
Aggregate-reactivation activity of the molecular chaperone ClpB from Ehrlichia chaffeensis

Zhang, Ting; Kedzierska-Mieszkowska, Sabina; Liu, Huitao; Cheng, Chuanmin; Ganta, Roman R.; Zolkiewski, Michal (2013-05-07)

Rickettsiale diseases, including human monocytic ehrlichiosis caused by Ehrlichia chaffeensis, are the second leading cause of the tick-borne infections in the USA and a growing health concern. Little is known about how ...
Allosteric Regulation of Fibronectin/alpha(5)beta(1) Interaction by Fibronectin-Binding MSCRAMMs

Liang, X. W.; Garcia, Brandon L.; Visai, L.; Prabhakaran, S.; Meenan, N. A. G.; Potts, J. R.; Humphries, M. J.; Hook, M.

Adherence ofmicrobes to host tissues is a hallmark of infectious disease and is often mediated by a class of adhesins termed MSCRAMMs (Microbial Surface Components Recognizing Adhesive Matrix Molecules). Numerous pathogens ...
Allosteric Regulation of Fibronectin/α5 β1 Interaction by Fibronectin-Binding MSCRAMMs

Liang, X.; Garcia, Brandon L.; Visai, L.; Prabhakaran, S.; Meenan, N. A. G.; Potts, J. R.; Humphries, M. J.; Höök, M. (2016-07-19)

Adherence of microbes to host tissues is a hallmark of infectious disease and is often mediated by a class of adhesins termed MSCRAMMs (Microbial Surface Components Recognizing Adhesive Matrix Molecules). Numerous pathogens ...
Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

Perkins, S. J.; Wright, D. W.; Zhang, H. L.; Brookes, E. H.; Chen, Jianhan H.; Irving, T. C.; Krueger, S.; Barlow, D. J.; Edler, K. J.; Scott, D. J.; Terrill, N. J.; King, S. M.; Butler, P. D.; Curtis, J. E. (2016-09-26)

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic ...
Borrelia burgdorferi BBK32 Inhibits the Classical Pathway by Blocking Activation of the C1 Complement Complex

Garcia, Brandon L.; Zhi, H.; Wager, B.; Hook, M.; Skare, J. T. (2016-01-25)

Pathogens that traffic in blood, lymphatics, or interstitial fluids must adopt strategies to evade innate immune defenses, notably the complement system. Through recruitment of host regulators of complement to their surface, ...
Branched oligopeptides form nano-capsules with lipid vesicle characteristics

Sukthankar, Pinakin; Gudlur, Sushanth; Avila, L. Adriana; Whitaker, Susan K.; Katz, Benjamin B.; Hiromasa, Yasuaki; Gao, Jian; Thapa, Prem; Moore, David; Iwamoto, Takeo; Chen, Jianhan; Tomich, John M. (2014-01-31)

In a recent article (Gudlur et al. PLOS ONE, 2012, 7 (9) e45374), we described the special properties of a mixed branched peptide assembly in which equimolar bis(FLIVI)-K-KKKK and bis(FLIVIGSII)-K-KKKK self-associate to ...
Channel replacement therapy for cystic fibrosis

Tomich, John M.; Bukovnik, Urska; Layman, Jammie; Schultz, Bruce D. (InTech, 2012-07-02)
Chemical warfare agent simulants in Gamble’s fluid: Is the fluid toxic? Can it be made safer by inclusion of solid nanocrystalline metal oxides?

Karote, Dennis; Walker, Brandon; Dai, Huaien; Krishnamoorthi, Ramaswamy; Voo, Janis; Rajagopalan, Shyamala (2012-12-05)

The reactions of chemical warfare agent simulants, 2-chloroethyl ethyl sulfide (2-CEES) and di-i-propyl fluoro phosphate (DFP), in fluids have been investigated. Data analyses confirm the major degradation pathway to be ...
Concerted loop motion triggers induced fit of FepA to ferric enterobactin

Smallwood, Chuck R.; Jordan, Lorne; Trinh, Vy; Schuerch, Daniel W.; Gala, Amparo; Hanson, Mathew; Shipelskiy, Yan; Majumdar, Aritri; Newton, Salete M.; Klebba, Phillip E. (2014-06-30)

Spectroscopic analyses of fluorophore-labeled Escherichia coli FepA described dynamic actions of its surface loops during binding and transport of ferric enterobactin (FeEnt). When FeEnt bound to fluoresceinated FepA, in ...
Confined Mobility of TonB and FepA in Escherichia coli Membranes

Lill, Y.; Jordan, L. D.; Smallwood, C. R.; Newton, Salete M.; Lill, M. A.; Klebba, Phillip E.; Ritchie, K. (2016-12-06)

The important process of nutrient uptake in Escherichia coli, in many cases, involves transit of the nutrient through a class of beta-barrel proteins in the outer membrane known as TonB-dependent transporters (TBDTs) and ...
CRISPR-UnLOCK: Multipurpose Cas9-Based Strategies for Conversion of Yeast Libraries and Strains

Roggenkamp, Emily; Giersch, Rachael M.; Wedeman, Emily; Eaton, Muriel; Turnquist, Emily; Schrock, Madison N.; Alkotami, Linah; Jirakittisonthon, Thitikan; Schluter-Pascua, Samantha E.; Bayne, Gareth H.; Wasko, Cory; Halloran, Megan; Finnigan, Gregory C. (2017-09-20)

Saccharomyces cerevisiae continues to serve as a powerful model system for both basic biological research and industrial application. The development of genome-wide collections of individually manipulated strains (libraries) ...
Cuticular protein with a low complexity sequence becomes cross-linked during insect cuticle sclerotization and is required for the adult molt

Mun, S.; Noh, M. Y.; Dittmer, Neal Thomas; Muthukrishnan, Subbaratnam; Kramer, K. J.; Kanost, Michael R.; Arakane, Yasuyuki (2015-05-21)
Defining the extreme substrate specificity of Euonymus alatus diacylglycerol acetyltransferase, an unusual membrane-bound O-acyltransferase

Bansal, Sunil; Durrett, Timothy P. (2016-11-08)

Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) synthesizes the unusually structured 3-acetyl-1,2-diacylglycerols (acetyl-TAG) found in the seeds of a few plant species. A member of the membrane-bound O-acyltransferase ...
Effect of diaminopropionic acid (Dap) on the biophysical properties of a modified synthetic channel-forming peptide

Bukovnik, Urska; Sala-Rabanal, Monica; Francis, Simonne; Frazier, Shawnalea J.; Schultz, Bruce D.; Nichols, Colin G.; Tomich, John M. (2013-09-06)

Channel replacement therapy, based on synthetic channel-forming peptides (CFPs) with the ability to supersede defective endogenous ion channels, is a novel treatment modality that may augment existing interventions against ...
Effects of flanking loops on membrane insertion of transmembrane helices: a role for peptide conformational equilibrium

Gao, Jian; Chen, Jianhan (2013-06-10)

The ability of a transmembrane helix (TMH) to insert into a lipid bilayer has been mainly understood based on the total hydrophobicity of the peptide sequence. Recently, Hedin et al. investigated the influence of flanking ...
Efficiency of adaptive temperature-based replica exchange for sampling large-scale protein conformational transitions

Zhang, Weihong; Chen, Jianhan (2013-05-02)

Temperature‐based replica exchange (RE) is now considered a principal technique for enhanced sampling of protein conformations. It is also recognized that existence of sharp cooperative transitions (such as protein ...
Electrostatically accelerated encounter and folding for facile recognition of intrinsically disordered proteins

Ganguly, Debabani; Zhang, Weihong; Chen, Jianhan (2013-11-23)

Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and ...
Force-induced unfolding simulations of the human Notch1 negative negulatory negion: Possible roles of the heterodimerization domain in mechanosensing

Chen, Jianhan; Zolkiewska, Anna (2011-07-28)

Notch receptors are core components of the Notch signaling pathway and play a central role in cell fate decisions during development as well as tissue homeostasis. Upon ligand binding, Notch is sequentially cleaved at the ...