Direct folding simulation of helical proteins using an effective polarizable bond force field
文献信息
Tong Zhu, Qinggang Zhang
We report a direct folding study of seven helical proteins (2I9M, Trpcage, 1WN8, C34, N36, 2KES, 2KHK) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.
期刊推荐

Acta Metallurgica Sinica-English Letters

Bioorganic & Medicinal Chemistry

Critical Reviews in Solid State and Materials Sciences

Biocatalysis and Biotransformation

NDT & E International

Herald of the Russian Academy of Sciences

Journal of the Indian Institute of Science

Cellulose

Medicinal Chemistry Research

Colloid Journal
相关文献
Tetra-substituted furans by a gold-catalysed tandem C(sp3)–H alkynylation/oxy-alkynylation reaction
Chunyu Han, Xianhai Tian, Lina Song, Yaowen Liu
DOI: 10.1039/D1QO01401C
Transition-metal-free hydroamination/defluorination/cyclization of perfluoroalkyl alkynes with amidines
Li-Wen Sun, Zi-Lun Yu, Xin-Long Luo, Mengtao Ma, Zhi-Liang Shen, Xue-Qiang Chu
DOI: 10.1039/D1QO01439K
Semi-syntheses of the 11-hydroxyrotenoids sumatrol and villosinol
David A. Russell, Julien J. Freudenreich, Hannah L. Stewart, Andrew D. Bond, Hannah F. Sore, David R. Spring
DOI: 10.1039/C8OB01919C
Decarbonylative Sonogashira cross-coupling: a fruitful marriage of alkynes with carboxylic acid electrophiles
Michal Szostak
DOI: 10.1039/D1QO01539G
A desulphurization strategy for Sonogashira couplings by visible light/copper catalysis
Xuan Li, Xiaolong Zhu, Xiuyan Song, Qirong Deng, Jian Lv
DOI: 10.1039/D1QO01548F
Electrophilic N-trifluoromethylthiophthalimide as a fluorinated reagent in the synthesis of acyl fluorides
Chen Zhu, Serik Zhumagazy, Huifeng Yue, Magnus Rueping
DOI: 10.1039/D1QO01633D
Synthesis of δ-phosphorothiolated alcohols by photoredox/copper catalyzed remote C(sp3)–H phosphorothiolation of N-alkoxypyridinium salts
Zhipeng Zheng, Shanshan Shi, Qianru Ma, Yufei Yang, Yan Liu, Guo Tang
DOI: 10.1039/D1QO01178B
您可能还喜欢
如何处理含有8-氯咪唑并[1,2-A]吡嗪(CAS号:69214-33-1)的废料?
处理含有8-氯咪唑并[1,2-A]吡嗪的废料时,应首先将其收集并进行化学回收或降解。如果无法回收,需采用安全的化学处理方法,如中和、氧化还原或沉淀。处理过程中需...
Calhex 231 hydrochloride(CAS号:2387505-78-2)适用哪些法规指南?
Calhex 231 hydrochloride 需要遵循《全球化学品统一分类和标签制度》(GHS)的分类和标签要求,以及欧盟的《化学品注册、评估、授权和限制条...
11-Beta,17-alpha,21-三羟基-5-beta-孕烯-3,20-二酮(CAS号:1482-50-4)的物理化学性质是什么?
11-Beta,17-alpha,21-三羟基-5-beta-孕烯-3,20-二酮是一种无色结晶性粉末,分子量为372.45 g/mol。该化合物在水中的溶解度...
处理5-异丙基-1,3,4-恶二唑-2-羧酸(CAS号:944907-13-5)时应注意哪些实验室安全事项?
处理5-异丙基-1,3,4-恶二唑-2-羧酸时应注意以下安全事项:穿戴适当的个人防护装备,包括实验室外套、手套和护目镜;操作应在通风橱中进行,以减少吸入或接触有...
benzyl 3-bromopropanoate(CAS号:90841-55-7)安全吗?
Benzyl 3-bromopropanoate属于有毒物质,吸入、摄入或皮肤接触均可能对人体造成伤害。操作时应佩戴防护眼镜、口罩和手套,避免吸入蒸汽和直接接触...
什么是(R)-N-苄氧羰基-3,4-二氢-1H-异喹啉羧酸(CAS号:151004-88-5)?
(R)-N-苄氧羰基-3,4-二氢-1H-异喹啉羧酸是一种含有苄氧羰基和异喹啉环结构的化合物,分子式为C17H15NO3。它是一种有机化合物,具有一定的生物活性...
在合成中是否有1-苄基吡啶嗡-3-羧酸盐(CAS号:15990-43-9)的替代品?
可以考虑使用1-苄基吡啶-3-羧酸盐作为1-苄基吡啶嗡-3-羧酸盐的替代品。此外,还可以探索其他类似物,如1-苄基吡啶-3-氨基甲酸酯等。具体的替代品选择需根据...
(2,6-二甲基吡啶-3-基)甲醇(CAS号:582303-10-4)安全吗?
(2,6-二甲基吡啶-3-基)甲醇在使用时需注意安全,应避免吸入其蒸汽,接触皮肤和眼睛。操作应在通风良好的环境中进行,佩戴适当的个人防护装备。
5-溴-2-乙烯基吡啶(CAS号:226883-52-9)的物理化学性质是什么?
5-溴-2-乙烯基吡啶是一种有机化合物,外观为白色固体,具有良好的结晶性。分子量约为190.03 g/mol。它的溶解性在水中较差,但在有机溶剂如二氯甲烷、甲醇...
2-羟基-3-硝基-5-甲基吡啶(CAS号:7464-14-4)应用于哪些行业?
2-羟基-3-硝基-5-甲基吡啶主要应用于医药、聚合物和半导体行业。在医药领域,它可以用作合成其他药物的中间体。在聚合物领域,它可以作为功能性单体参与聚合反应,...
来源期刊
Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

![Ethyl 3-((6-(4,5-dihydro-1H-benzo[d]azepin-3(2H)-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoate structure Ethyl 3-((6-(4,5-dihydro-1H-benzo[d]azepin-3(2H)-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoate structure](https://cnstatic.chemtradehub.com/structs/137/1373423-53-0-496a.webp)


