Protein dynamics underlying allosteric regulation.

Curr Opin Struct Biol

Center for Computational Biology, Flatiron Institute, New York, NY, USA; Center for Computational Mathematics, Flatiron Institute, New York, NY, USA. Electronic address:

Published: February 2024

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Advances in structure-based allosteric drug design.

Curr Opin Struct Biol

December 2024

State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Protection, Development, and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptides & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China. Electronic address:

The identification of allosteric binding sites forms a critical connection between structural and computational biology, substantially advancing the discovery of allosteric drugs. However, the prevailing strategies for allosteric drug development predominantly rely on high-throughput screening, which suffers from high failure rates due to a limited understanding of allosteric mechanisms. This review collects insights from case studies on allosteric mechanisms, protein structure databases and computation algorithm developments, aiming to enhance our comprehension of allostery and guide more effective allosteric drug development.

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The rapid identification of protein-protein interactions has been significantly enabled by mass spectrometry (MS) proteomics-based methods, including affinity purification-MS, crosslinking-MS, and proximity-labeling proteomics. While these methods can reveal networks of interacting proteins, they cannot reveal how specific protein-protein interactions alter protein function or cell signaling. For instance, when two proteins interact, there can be emergent signaling processes driven purely by the individual activities of those proteins being co-localized.

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A PDZ-kinase allosteric relay mediates Par complex regulator exchange.

J Biol Chem

December 2024

Department of Chemistry and Biochemistry, Institute of Molecular Biology, 1229 University of Oregon, Eugene, Oregon, USA. Electronic address:

The Par complex polarizes the plasma membrane of diverse animal cells using the catalytic activity of atypical PKC (aPKC) to pattern substrates. Two upstream regulators of the Par complex, Cdc42 and Par-3, bind separately to the complex to influence its activity in different ways. Each regulator binds a distinct member of the complex, Cdc42 to Par-6 and Par-3 to aPKC, making it unclear how they influence one another's binding.

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This review documents investigations leading to the unprecedented discovery of filamentation as a mode of enzyme regulation in the type II restriction endonuclease SgrAI. Filamentation is defined here as linear or helical polymerization of a single enzyme as occurs for SgrAI, and has now been shown to occur in many other enzyme systems, including conserved metabolic enzymes. In the case of SgrAI, filamentation activates the DNA cleavage rate by up to 1000-fold and also alters the enzyme's DNA sequence specificity.

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Agonists enhance receptor activity by providing net-favorable binding energy to active over resting conformations, with efficiency (η) linking binding energy to gating. Previously, we showed that in nicotinic receptors, η-values are grouped into five structural pairs, correlating efficacy and affinity within each class, uniting binding with allosteric activation (Indurthi and Auerbach, 2023). Here, we use molecular dynamics (MD) simulations to investigate the low-to-high affinity transition (L→H) at the Torpedo α-δ nicotinic acetylcholine receptor neurotransmitter site.

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