Search Results - "Nussinov, Ruth"

Allostery: An Overview of Its History, Concepts, Methods, and Applications by Liu, Jin, Nussinov, Ruth

“…The concept of allostery has evolved in the past century. In this Editorial, we briefly overview the history of allostery, from the pre-allostery nomenclature…”
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Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell by Wei, Guanghong, Xi, Wenhui, Nussinov, Ruth, Ma, Buyong

“…All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic…”
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A unified view of "how allostery works" by Tsai, Chung-Jung, Nussinov, Ruth

“…The question of how allostery works was posed almost 50 years ago. Since then it has been the focus of much effort. This is for two reasons: first, the…”
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Advancements and challenges in computational biology by Nussinov, Ruth

“…  [...]studying the dynamics of large integrated models is increasingly used to improve our understanding of how large complexes function in the cell and how…”
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Induced fit, conformational selection and independent dynamic segments: an extended view of binding events by Csermely, Peter, Palotai, Robin, Nussinov, Ruth

“…Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here, we describe an extended conformational…”
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The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B by Lu, Shaoyong, Jang, Hyunbum, Nussinov, Ruth, Zhang, Jian

“…Ras mediates cell proliferation, survival and differentiation. Mutations in K-Ras4B are predominant at residues G12, G13 and Q61. Even though all impair…”
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Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane by Zhang, Mingzhen, Zheng, Jie, Nussinov, Ruth, Ma, Buyong

“…How cytochrome C is released from the mitochondria to the cytosol via Bax oligomeric pores, a process which is required for apoptosis, is still a mystery…”
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Allostery without a conformational change? Revisiting the paradigm by Nussinov, Ruth, Tsai, Chung-Jung

“…•Classically, allostery induces a functional switch through a conformational change.•Lately numerous studies concluded that allostery takes place through…”
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Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view by Lu, Shaoyong, Jang, Hyunbum, Gu, Shuo, Zhang, Jian, Nussinov, Ruth

“…Ras proteins are small GTPases, cycling between inactive GDP-bound and active GTP-bound states. Through these switches they regulate signaling that controls…”
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Ras Conformational Ensembles, Allostery, and Signaling by Lu, Shaoyong, Jang, Hyunbum, Muratcioglu, Serena, Gursoy, Attila, Keskin, Ozlem, Nussinov, Ruth, Zhang, Jian

“…Ras proteins are classical members of small GTPases that function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states…”
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Enzyme dynamics point to stepwise conformational selection in catalysis by Ma, Buyong, Nussinov, Ruth

“…Recent data increasingly reveal that conformational dynamics are indispensable to enzyme function throughout the catalytic cycle, in substrate recruiting,…”
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Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics by Maximova, Tatiana, Moffatt, Ryan, Ma, Buyong, Nussinov, Ruth, Shehu, Amarda

“…Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant…”
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Artificial intelligence in COVID-19 drug repurposing by Zhou, Yadi, Wang, Fei, Tang, Jian, Nussinov, Ruth, Cheng, Feixiong

“…Drug repurposing or repositioning is a technique whereby existing drugs are used to treat emerging and challenging diseases, including COVID-19. Drug…”
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Energetic redistribution in allostery to execute protein function by Liu, Jin, Nussinov, Ruth

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Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM by Tuncbag, Nurcan, Gursoy, Attila, Nussinov, Ruth, Keskin, Ozlem

“…Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps…”
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Network approaches and applications in biology by Ideker, Trey, Nussinov, Ruth

“…About the Authors: Trey Ideker * E-mail: tideker@ucsd.edu (TI); NussinoR@mail.nih.gov (RN) Affiliation: Department of Medicine, University of California San…”
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Computational network biology: Data, models, and applications by Liu, Chuang, Ma, Yifang, Zhao, Jing, Nussinov, Ruth, Zhang, Yi-Cheng, Cheng, Feixiong, Zhang, Zi-Ke

“…Biological entities are involved in intricate and complex interactions, in which uncovering the biological information from the network concepts are of great…”
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Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states by Miller, Yifat, Ma, Buyong, Nussinov, Ruth, Stanley, H. Eugene

“…Although a key factor in Alzheimer's disease etiology is enrichment of Zn²⁺ in aggregates, and there are data suggesting that zinc promotes aggregation, how…”
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The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery by Papaleo, Elena, Saladino, Giorgio, Lambrughi, Matteo, Lindorff-Larsen, Kresten, Gervasio, Francesco Luigi, Nussinov, Ruth

“…Proteins are dynamic entities that undergo a plethora of conformational changes that may take place on a wide range of time scales. These changes can be as…”
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Phosphorylated Calmodulin Promotes PI3K Activation by Binding to the SH2 Domains by Zhang, Mingzhen, Jang, Hyunbum, Gaponenko, Vadim, Nussinov, Ruth

“…How calmodulin (CaM) acts in KRAS-driven cancers is a vastly important question. CaM binds to and stimulates PI3Kα/Akt signaling, promoting cell growth and…”
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