Applications of a Single Molecule Theory of Protein Dynamics

A single molecule theory for protein dynamics has been developed since 2012. It consists of the concepts of conformational Gibbs free energy function (CGF) and single molecule thermodynamic hypothesis (STH) that claims that all stable conformations are (local or global) minimizers of CGF. These are enough to give a unified explanations and mechanisms to many aspects of protein dynamics such as protein folding;allostery;denaturation;and intrinsically disordered proteins. Formulas of CGF in water environment had been derived via quantum statistics. Applications of them to soluble proteins are: docking Gibbs free energy difference formula and a practical way to search better docking site;single molecule binding affinity;predicting and explaining why structures of a monomeric globular protein looks like a globule and is tightly packed with a hydrophobic core;a representation of the hydrophobic effect;and a wholistic view to structures of water soluble proteins.

Androgen receptor co-regulation in prostate cancer

Prostate cancer(PCa)progression relies on androgen receptor(AR)action.Preventing AR’s ligand-activation is the frontline treatment for metastatic PCa.Androgen deprivation therapy(ADT)that inhibits AR ligand-binding initially induces remission but eventually fails,mainly because of adaptive PCa responses that restore AR action.The vast majority of castration-resistant PCa(CRPC)continues to rely on AR activity.Novel therapeutic strategies are being explored that involve targeting other critical AR domains such as those that mediate its constitutively active transactivation function,its DNA binding ability,or its interaction with co-operating transcriptional regulators.Considerable molecular and clinical variability has been found in AR’s interaction with its ligands,DNA binding motifs,and its associated coregulators and transcription factors.Here,we review evidence that each of these levels of AR regulation can individually and differentially impact transcription by AR.In addition,we examine emerging insights suggesting that each can also impact the other,and that all three may collaborate to induce gene-specific AR target gene expression,likely via AR allosteric effects.For the purpose of this review,we refer to the modulating influence of these differential and/or interdependent contributions of ligands,cognate DNA-binding motifs and critical regulatory protein interactions on AR’s transcriptional output,which may influence the efficiency of the novel PCa therapeutic approaches under consideration,as co-regulation of AR activity.

Mapping allosteric pathway in NIa-Pro using computational approach

Background:Computer simulation studies complement in vitro experiments and provide avenue to understand allosteric regulation in the absence of other molecular viewing techniques.Molecular dynamics captures internal motion within the protein and enables tracing the communication path between a catalytic site and a distal allosteric site.In this article,we have identified the communication pathway between the viral protein genome linked(VPg)binding region and catalytic active site in nuclear inclusion protein-a protease(NIa-Pro).Methods:Molecular dynamics followed by in silico analyses have been used to map the allosteric pathway.Results:This study delineates the residue interaction network involved in allosteric regulation of NIa-Pro activity by VPg.Simulation studies indicate that point mutations in the VPg interaction interface of NIa-Pro lead to disruption in these networks and change the orientation of catalytic residues.His142Ala and His167Ala mutations do not show a substantial change in the overall protease structure,but rather in the residue interaction network and catalytic site geometry.Conclusion:Our mutagenic study delineates the allosteric pathway and facilitates the understanding of the modulation of NIa-Pro activity on a molecular level in the absence of the structure of its complex with the known regulator VPg.Additionally,our in silico analysis explains the molecular concepts and highlights the dynamics behind the previously reported wet lab study findings.

通道S1–S4显著的动态变化而非静止状态是香草素类配体激活TRPV1的关键因素

瞬时受体电位香草素1(TRPV1)通道参与了哺乳动物体内许多重要的生理和病理过程,对其门控机制的全面了解有助于为相关疾病的治疗干预提供可能.近年来冷冻电子显微镜(cryo-EM)技术在结构生物学中取得了惊人的成果,所有TRPV亚型(TRPV1±6)的高分辨率结构也得到了解析:它们都具有高度保守的6个跨膜(TM)结构域(S1±S6),与电压门控离子通道(VGICs)相似.并且,在结合了香草素激动剂(辣椒素或树脂毒素)的TRPV1通道开放结构中,TM螺旋S1±S4形成一束,保持静止状态,这也证明了TRP和VGICs通道功能和门控机制的差异.然而,本研究认为S1±S4的动态变化而非静止是辣椒素激活TRPV1的必要条件.通过荧光非天然氨基酸结合和电压钳荧光测量分析,本研究直接观察到辣椒素结合后S1±S4域的运动.电压钳荧光测量法(VCF)所识别位点的化学修饰、单通道记录、细胞凋亡分析和对一种新激动剂PSFL828作用的探索,共同证实了这种协调的S1±S4运动在辣椒素介导的TRPV1激活中的重要作用.这项研究提出了一个新的见解:与冷冻电镜结构研究的结论不同,香草素激动剂在TRPV1激活过程中也需要S1±S4运动.本文重新定义香草素类激动剂的门控过程并发现了新的非香草素类激动剂,为开发TRPV1调节剂提供了新策略.

Targeting RAS phosphorylation in cancer therapy:Mechanisms and modulators

RAS,a member of the small GTPase family,functions as a binary switch by shifting between inactive GDP-loaded and active GTP-loaded state.RAS gain-of-function mutations are one of the leading causes in human oncogenesis,accounting for w19%of the global cancer burden.As a well-recognized target in malignancy,RAS has been intensively studied in the past decades.Despite the sustained efforts,many failures occurred in the earlier exploration and resulted in an‘undruggable’feature of RAS proteins.Phosphorylation at several residues has been recently determined as regulators for wild-type and mutated RAS proteins.Therefore,the development of RAS inhibitors directly targeting the RAS mutants or towards upstream regulatory kinases supplies a novel direction for tackling the anti-RAS difficulties.A better understanding of RAS phosphorylation can contribute to future therapeutic strategies.In this review,we comprehensively summarized the current advances in RAS phosphorylation and provided mechanistic insights into the signaling transduction of associated pathways.Importantly,the preclinical and clinical success in developing anti-RAS drugs targeting the upstream kinases and potential directions of harnessing allostery to target RAS phosphorylation sites were also discussed.

Targeting a cryptic allosteric site of SIRT6 with small-molecule inhibitors that inhibit the migration of pancreatic cancer cells

SIRT6 belongs to the conserved NAD^(+)-dependent deacetylase superfamily and mediates multiple biological and pathological processes.Targeting SIRT6 by allosteric modulators represents a novel direction for therapeutics,which can overcome the selectivity problem caused by the structural similarity of orthosteric sites among deacetylases.Here,developing a reversed allosteric strategy Allo Reverse,we identified a cryptic allosteric site,Pocket Z,which was only induced by the bi-directional allosteric signal triggered upon orthosteric binding of NAD^(+).Based on Pocket Z,we discovered an SIRT6 allosteric inhibitor named JYQ-42.JYQ-42 selectively targets SIRT6 among other histone deacetylases and effectively inhibits SIRT6 deacetylation,with an IC50 of 2.33μmol/L.JYQ-42 significantly suppresses SIRT6-mediated cancer cell migration and pro-inflammatory cytokine production.JYQ-42,to our knowledge,is the most potent and selective allosteric SIRT6 inhibitor.This study provides a novel strategy for allosteric drug design and will help in the challenging development of therapeutic agents that can selectively bind SIRT6.

Dynamical and allosteric regulation of photoprotection in light harvesting complex Ⅱ

Major light-harvesting complex of photosystemⅡ(LHCⅡ)plays a dual role in light-harvesting and excited energy dissipation to protect photodamage from excess energy.The regulatory switch is induced by increased acidity,temperature or both.However,the molecular origin of the protein dynamics at the atomic level is still unknown.We carried out temperature-jump time-resolved infrared spectroscopy and molecular dynamics simulations to determine the energy quenching dynamics and conformational changes of LHCⅡtrimers.We found that the spontaneous formation of a pair of localα-helices from the 310-helix E/loop and the C-terminal coil of the neighboring monomer,in response to the increased environmental temperature and/or acidity,induces a scissoring motion of transmembrane helices A and B,shifting the conformational equilibrium to a more open state,with an increased angle between the associated carotenoids.The dynamical and allosteric conformation change leads to close contacts between carotenoid lutein 1 and chlorophyll pigment 612,facilitating the fluorescence quenching.Based on these results,we suggest a unified mechanism by which the LHCⅡtrimer controls the dissipation of excess excited energy in response to increased temperature and acidity,as an intrinsic result of intense sun light in plant photosynthesis.