Center for Computational Biology Scholarly Works
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Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search
(Nature Research, 2022-10-12)AlphaFold can predict the structure of single- and multiple-chain proteins with very high accuracy. However, the accuracy decreases with the number of chains, and the available GPU memory limits the size of protein complexes ... -
GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes
(2022-06-15)Rapid progress in structural modeling of proteins and their interactions is powered by advances in knowledge-based methodologies along with better understanding of physical principles of protein structure and function. The ... -
DOCKGROUND membrane protein-protein set
(Public Library of Science, 2022-05-17)Membrane proteins are significantly underrepresented in Protein Data Bank despite their essential role in cellular mechanisms and the major progress in experimental protein structure determination. Thus, computational ... -
Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives
(Dove Medical Press, 2021-02-20)Biomolecular recognition such as binding of small molecules, nucleic acids, peptides and proteins to their target receptors plays key roles in cellular function and has been targeted for therapeutic drug design. Molecular ... -
Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations
(Cell Press, 2021-03-19)Here, we describe a generic protocol for monitoring protein-RNA interaction using a cleavable GFP fusion of a recombinant RNA-binding protein. We detail each expression and purification step, including high salt and heparin ... -
A clinically relevant polymorphism in the Na+/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position
(Elsevier, 2020-11-09)Conventionally, most amino acid substitutions at “important” protein positions are expected to abolish function. However, in several soluble-globular proteins, we identified a class of nonconserved positions for which ... -
Costameric integrin and sarcoglycan protein levels are altered in a Drosophila model for Limb-girdle muscular dystrophy type 2H
(Springer Nature, 2021-01-28)Mutations in two different domains of the ubiquitously expressed TRIM32 protein give rise to two clinically separate diseases, one of which is Limb-girdle muscular dystrophy type 2H (LGMD2H). Uncovering the muscle-specific ... -
Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor
(Frontiers Media, 2021-04-27)Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the ... -
Machine learning differentiates enzymatic and non-enzymatic metals in proteins
(Nature Research, 2021-06-17)Metalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. Because of the physicochemical similarities between the active sites of metalloenzymes and inactive metal binding sites, it is ... -
Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness
(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
(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
(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
(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
(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
(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
(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
(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
(Public Library of Science, 2017-01-19) -
Crosstalk and the evolvability of intracellular communication
(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
(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 ...
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