Browse by

 

 

Recent Submissions

  • Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness 

    Phillips, Kelly N.; Widmann, Scott; Lai, Huei-Yi; Nguyen, Jennifer; Ray, J. Christian J.; Balázsi, Gábor; Cooper, Tim F. (American Society for Microbiology, 2019-11-12)
    Transcription of bacterial genes is controlled by the coordinated action of cis- and trans-acting regulators. The activity and mode of action of these regulators can reflect different requirements for gene products in ...
  • Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics 

    Ricci, Clarisse G.; Chen, Janice S.; Miao, Yinglong; Jinek, Martin; Doudna, Jennifer A.; McCammon, J. Andrew; Palermo, Giulia (American Chemical Society, 2019-03-07)
    CRISPR-Cas9 is the state-of-the-art technology for editing and manipulating nucleic acids. However, the occurrence of off-target mutations can limit its applicability. Here, all-atom enhanced molecular dynamics (MD) ...
  • A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core Motif 

    Utesch, Tillmann; de Miguel Catalina, Alejandra; Schattenberg, Caspar; Paege, Norman; Schmieder, Peter; Krause, Eberhard; Miao, Yinglong; McCammon, J. Andrew; Meyer, Vera; Jung, Sascha; Mroginski, Maria Andrea (American Society for Microbiology, 2018-10-03)
    Fungal pathogens kill more people per year globally than malaria or tuberculosis and threaten international food security through crop destruction. New sophisticated strategies to inhibit fungal growth are thus urgently ...
  • Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor 

    Miao, Yinglong; Bhattarai, Apurba; Nguyen, Anh T. N.; Christopoulos, Arthur; May, Lauren T. (Nature Research, 2018-11-15)
    Despite intense interest in designing positive allosteric modulators (PAMs) as selective drugs of the adenosine A1 receptor (A1AR), structural binding modes of the receptor PAMs remain unknown. Using the first X-ray structure ...
  • Quantitative Genetic Mapping and Genome Assembly in the Lesser Wax Moth Achroia grisella 

    Koseva, Boryana S.; Hackett, Jennifer L.; Zhou, Yihong; Harris, Bethany R.; Kelly, John K.; Greenfield, Michael D.; Gleason, Jennifer M.; Macdonald, Stuart J. (Genetics Society of America, 2019-05-17)
    Specific characteristics of the male Achroia grisella acoustic mating signal determine a male’s attractiveness toward females. These features are genetically variable in populations, and mapping experiments have been used ...
  • Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction 

    Lan, Lan; Liu, Jiajun; Xing, Minli; Smith, Amber R.; Wang, Jinan; Wu, Xiaoqing; Appelman, Carl; Li, Ke; Roy, Anuradha; Gowthaman, Ragul; Karanicolas, John; Somoza, Amber D.; Wang, Clay C. C.; Miao, Yinglong; Guzman, Roberto De; Oakley, Berl R.; Neufeld, Kristi L.; Xu, Liang (Wiley, 2020-08-08)
    RNA-binding protein Musashi-1 (MSI1) is a key regulator of several stem cell populations. MSI1 is involved in tumor proliferation and maintenance, and it regulates target mRNAs at the translational level. The known mRNA ...
  • Modulating Integrin αIIbβ3 Activity through Mutagenesis of Allosterically Regulated Intersubunit Contacts 

    Tan, Sophia K.; Fong, Karen P.; Polizzi, Nicholas F.; Sternisha, Alex; Slusky, Joanna S. G.; Yoon, Kyungchul; DeGrado, William F.; Bennett, Joel S. (American Chemical Society, 2019-07-02)
    Integrin αIIbβ3, a transmembrane heterodimer, mediates platelet aggregation when it switches from an inactive to an active ligand-binding conformation following platelet stimulation. Central to regulating αIIbβ3 activity ...
  • Cooperativity in Proteasome Core Particle Maturation 

    Suppahia, Anjana; Itagi, Pushpa; Burris, Alicia; Kim, Faith Mi Ge; Vontz, Alexander; Kante, Anupama; Kim, Seonghoon; Im, Wonpil; Deeds, Eric J.; Roelofs, Jeroen (Elsevier, 2020-04-22)
    Proteasomes are multi-subunit protease complexes found in all domains of life. The maturation of the core particle (CP), which harbors the active sites, involves dimerization of two half CPs (HPs) and an autocatalytic ...
  • Computing the Dynamic Supramolecular Structural Proteome 

    Nussinov, Ruth; Papin, Jason A.; Vakser, Ilya A. (Public Library of Science, 2017-01-19)
  • Crosstalk and the evolvability of intracellular communication 

    Rowland, Michael A.; Greenbaum, Joseph M.; Deeds, Eric J. (Nature Research, 2017-07-10)
    Metazoan signalling networks are complex, with extensive crosstalk between pathways. It is unclear what pressures drove the evolution of this architecture. We explore the hypothesis that crosstalk allows different cell ...
  • Fundamental trade-offs between information flow in single cells and cellular populations 

    Suderman, Ryan; Bachman, John A.; Smith, Adam; Sorger, Peter K.; Deeds, Eric J. (National Academy of Sciences, 2017-05)
    Signal transduction networks allow eukaryotic cells to make decisions based on information about intracellular state and the environment. Biochemical noise significantly diminishes the fidelity of signaling: networks ...
  • Lineage space and the propensity of bacterial cells to undergo growth transitions 

    Bandyopadhyay, Arnab; Wang, Huijing; Ray, J. Christian J. (Public Library of Science, 2018-08-22)
    The molecular makeup of the offspring of a dividing cell gradually becomes phenotypically decorrelated from the parent cell by noise and regulatory mechanisms that amplify phenotypic heterogeneity. Such regulatory mechanisms ...
  • Natural language processing in text mining for structural modeling of protein complexes 

    Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A. (BioMed Central, 2018-03-05)
    BACKGROUND: Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. ...
  • Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System 

    Nariya, Maulik K.; Israeli, Johnny; Shi, Jack J.; Deeds, Eric J. (Public Library of Science, 2016-04)
    Type III Secretion Systems (T3SS) are complex bacterial structures that provide gram-negative pathogens with a unique virulence mechanism whereby they grow a needle-like structure in order to inject bacterial effector ...
  • Structure Fluctuations and Conformational Changes in Protein Binding 

    Ruvinsky, Anatoly M.; Kirys, Tatsiana; Tuzikov, Alexander V.; Vakser, Ilya A. (World Scientific Publishing, 2012-04)
    Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the ...
  • Side-Chain Conformational Changes upon Protein-Protein Association 

    Ruvinsky, Anatoly M.; Kirys, Tatsiana; Tuzikov, Alexander V.; Vakser, Ilya A. (Elsevier, 2011-02-25)
    Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results ...
  • Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association 

    Wani, Prashant S.; Rowland, Michael A.; Ondracek, Alex; Deeds, Eric J.; Roelofs, Jeroen (Nature Publishing Group, 2015-03-16)
    Proteasome assembly is a complex process, requiring 66 subunits distributed over several subcomplexes to associate in a coordinated fashion. Ten proteasome-specific chaperones have been identified that assist in this ...
  • Transmembrane Helix Assembly by Window Exchange Umbrella Sampling 

    Park, Soohyung; Kim, Taehoon; Im, Wonpil (American Physical Society, 2012-03-08)
    A method of window exchange umbrella sampling molecular dynamics simulation is employed for transmembrane helix assembly. An analytical expression for the average acceptance probability between neighboring windows is derived ...
  • Template-Based Modeling of Protein-RNA Interactions 

    Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.; Liu, Shiyong (Public Library of Science, 2016-09-23)
    Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding ...