Search Results - "Fuentes, Ernesto J"

Hidden dynamic allostery in a PDZ domain by Petit, Chad M, Zhang, Jun, Sapienza, Paul J, Fuentes, Ernesto J, Lee, Andrew L

“…Structure-function relationships in proteins are predicated on the spatial proximity of noncovalently interacting groups of atoms. Thus, structural elements…”
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Conformational Dynamics and Cooperativity Drive the Specificity of a Protein-Ligand Interaction by Liu, Xu, Golden, Lisa C., Lopez, Josue A., Shepherd, Tyson R., Yu, Liping, Fuentes, Ernesto J.

“…Molecular recognition is critical for the fidelity of signal transduction in biology. Conversely, the disruption of protein-protein interactions can lead to…”
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A novel pathway spatiotemporally activates Rac1 and redox signaling in response to fluid shear stress by Liu, Yunhao, Collins, Caitlin, Kiosses, William B, Murray, Ann M, Joshi, Monika, Shepherd, Tyson R, Fuentes, Ernesto J, Tzima, Ellie

“…Hemodynamic forces regulate embryonic organ development, hematopoiesis, vascular remodeling, and atherogenesis. The mechanosensory stimulus of blood flow…”
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Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions by Liu, Xu, Speckhard, David C., Shepherd, Tyson R., Sun, Young Joo, Hengel, Sarah R., Yu, Liping, Fowler, C. Andrew, Gakhar, Lokesh, Fuentes, Ernesto J.

“…Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used…”
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The Structure of the Tiam1 PDZ Domain/ Phospho-Syndecan1 Complex Reveals a Ligand Conformation that Modulates Protein Dynamics by Liu, Xu, Shepherd, Tyson R., Murray, Ann M., Xu, Zhen, Fuentes, Ernesto J.

“…PDZ (PSD-95/Dlg/ZO-1) domains are protein-protein interaction modules often regulated by ligand phosphorylation. Here, we investigated the specificity,…”
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Conservation of Side-Chain Dynamics Within a Protein Family by Law, Anthony B, Fuentes, Ernesto J, Lee, Andrew L

“…The question of protein dynamics and its relevance to function is currently a topic of great interest. Proteins are particularly dynamic at the side-chain…”
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Emerging Themes in PDZ Domain Signaling: Structure, Function, and Inhibition by Liu, Xu, Fuentes, Ernesto J

“…Post-synaptic density-95, disks-large and zonula occludens-1 (PDZ) domains are small globular protein-protein interaction domains widely conserved from yeast…”
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Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein by Fuentes, Ernesto J., Gilmore, Steven A., Mauldin, Randall V., Lee, Andrew L.

“…A number of computational and experimental studies have identified intramolecular communication “pathways” or “networks” important for transmitting allostery…”
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Distinct Ligand Specificity of the Tiam1 and Tiam2 PDZ Domains by Shepherd, Tyson R, Hard, Ryan L, Murray, Ann M, Pei, Dehua, Fuentes, Ernesto J

“…Guanine nucleotide exchange factor proteins of the Tiam family are activators of the Rho GTPase Rac1 and critical for cell morphology, adhesion, migration, and…”
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Specificity residues determine binding affinity for two-component signal transduction systems by Willett, Jonathan W, Tiwari, Nitija, Müller, Susanne, Hummels, Katherine R, Houtman, Jon C D, Fuentes, Ernesto J, Kirby, John R

“…Two-component systems (TCS) comprise histidine kinases and their cognate response regulators and allow bacteria to sense and respond to a wide variety of…”
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The Tiam1 PDZ Domain Couples to Syndecan1 and Promotes Cell–Matrix Adhesion by Shepherd, Tyson R., Klaus, Suzi M., Liu, Xu, Ramaswamy, S., DeMali, Kris A., Fuentes, Ernesto J.

“…The T-cell lymphoma invasion and metastasis gene 1 (Tiam1) is a guanine exchange factor (GEF) for the Rho-family GTPase Rac1 that is crucial for the integrity…”
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A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain by Panel, Nicolas, Sun, Young Joo, Fuentes, Ernesto J, Simonson, Thomas

“…PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands…”
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Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations by Panel, Nicolas, Villa, Francesco, Fuentes, Ernesto J., Simonson, Thomas

“…PDZ domains contain 80–100 amino acids and bind short C-terminal sequences of target proteins. Their specificity is essential for cellular signaling pathways…”
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Assessing the functional roles of coevolving PHD finger residues by Basu, Shraddha, Subedi, Ujwal, Tonelli, Marco, Afshinpour, Maral, Tiwari, Nitija, Fuentes, Ernesto J., Chakravarty, Suvobrata

“…Although in silico folding based on coevolving residue constraints in the deep‐learning era has transformed protein structure prediction, the contributions of…”
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The Staphylococcus aureus ArlRS two‐component system regulates virulence factor expression through MgrA by Crosby, Heidi A., Tiwari, Nitija, Kwiecinski, Jakub M., Xu, Zhen, Dykstra, Allison, Jenul, Christian, Fuentes, Ernesto J., Horswill, Alexander R.

“…Summary The Gram‐positive bacterium, Staphylococcus aureus, is a versatile pathogen that can sense and adapt to a wide variety of environments within the human…”
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Therapeutic Inhibition of Staphylococcus aureus ArlRS Two-Component Regulatory System Blocks Virulence by Kwiecinski, Jakub M, Jelani, Diamond A, Fuentes, Ernesto J, Horswill, Alexander R

“…Staphylococcus aureus is a common cause of severe infections, and its widespread antibiotic resistance necessitates search for alternative therapies, such as…”
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FBG1 is a promiscuous ubiquitin ligase that sequesters APC2 and causes S-phase arrest by Wen, Hsiang, Kim, Namhun, Fuentes, Ernesto J., Mallinger, Adam, Gonzalez-Alegre, Pedro, Glenn, Kevin A.

“…During cell proliferation, protein degradation is strictly regulated by the cell cycle and involves two complementary ubiquitin ligase complexes, the SCF (Skp,…”
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The SrrAB two-component system regulates Staphylococcus aureus pathogenicity through redox sensitive cysteines by Tiwari, Nitija, López-Redondo, Marisa, Miguel-Romero, Laura, Kulhankova, Katarina, Cahill, Michael P., Tran, Phuong M., Kinney, Kyle J., Kilgore, Samuel H., Al-Tameemi, Hassan, Herfst, Christine A., Tuffs, Stephen W., Kirby, John R., Boyd, Jeffery M., McCormick, John K., Salgado-Pabón, Wilmara, Marina, Alberto, Schlievert, Patrick M., Fuentes, Ernesto J.

“…Staphylococcus aureus infections can lead to diseases that range from localized skin abscess to life-threatening toxic shock syndrome. The SrrAB two-component…”
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The Tiam1 guanine nucleotide exchange factor is auto-inhibited by its pleckstrin homology coiled-coil extension domain by Xu, Zhen, Gakhar, Lokesh, Bain, Fletcher E., Spies, Maria, Fuentes, Ernesto J.

“…T-cell lymphoma invasion and metastasis 1 (Tiam1) is a Dbl-family guanine nucleotide exchange factor (GEF) that specifically activates the Rho-family GTPase…”
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A physics-based energy function allows the computational redesign of a PDZ domain by Opuu, Vaitea, Sun, Young Joo, Hou, Titus, Panel, Nicolas, Fuentes, Ernesto J., Simonson, Thomas

“…Computational protein design (CPD) can address the inverse folding problem, exploring a large space of sequences and selecting ones predicted to fold. CPD was…”
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