Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations
文献信息
Ubiquitin is a highly conserved, highly represented protein acting as a regulating signal in numerous cellular processes. It leverages a single hydrophobic binding patch to recognize and bind a large variety of protein domains with remarkable specificity, but can also self-assemble into chains of poly-diubiquitin units in which these interfaces are sequestered, profoundly altering the individual monomers' recognition characteristics. Despite numerous studies, the origins of this varied specificity and the competition between substrates for the binding of the ubiquitin interface patch remain under heated debate. This study uses enhanced sampling all-atom molecular dynamics to simulate the unbinding of complexes of mono- or K48-linked diubiquitin bound to several ubiquitin-associated domains, providing insights into the mechanism and free energetics of ubiquitin recognition and binding. The implications for the subtle tradeoff between the stability of the polyubiquitin signal and its easy recognition by target protein assemblies are discussed, as is the enhanced affinity of the latter for long polyubiquitin chains compared to isolated mono- or diubiquitin.
期刊推荐
相关文献
Enhancement of spin polarization induced by Coulomb on-site repulsion between localized pz electrons in graphene embedded with line defects
Zhigang Wang, Rui-Qin Zhang, Zejun Ding, Michel A. Van Hove
DOI: 10.1039/C5CP03764F
Ultrafast charge carrier relaxation and charge transfer processes in CdS/CdTe thin films
Ruvini Dharmadasa, I. M. Dharmadasa, Thad Druffel
DOI: 10.1039/C5CP01652E
Trap-limited charge recombination in intrinsic perovskite film and meso-superstructured perovskite solar cells and the passivation effect of the hole-transport material on trap states
Yi Wang, Hao-Yi Wang, Man Yu, Li-Min Fu, Yujun Qin, Jian-Ping Zhang, Xi-Cheng Ai
DOI: 10.1039/C5CP04360C
Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory
Wei Hu, Chao Yang
DOI: 10.1039/C5CP00333D
The R- and S-diastereoisomeric effects on the guanidinohydantoin-induced mutations in DNA
N. R. Jena, Vivek Gaur, P. C. Mishra
DOI: 10.1039/C5CP02636A
Sign change of magnetoresistance in Gd-doped amorphous carbon granular films
Shihao Ding, Chao Jin, Ziwei Fan, Peng Li, Haili Bai
DOI: 10.1039/C5CP05070G
Quantum dynamics of the photostability of pyrazine
Matthieu Sala, Stéphane Guérin, Fabien Gatti
DOI: 10.1039/C5CP04605J
Optimized multi-site local orbitals in the large-scale DFT program CONQUEST
Ayako Nakata
DOI: 10.1039/C5CP00934K
Facile synthesis of highly conductive sulfur-doped reduced graphene oxide sheets
Jitao Li, Gangyi Zhu, Junfeng Lu, Yueyue Wang, Zengliang Shi, Chunxiang Xu
DOI: 10.1039/C5CP05475C
您可能还喜欢
什么是2-氨基戊烷(CAS号:63493-28-7)?
2-氨基戊烷,又名pentan-2-amine,是一种有机化合物,分子式为C5H11NH2。它是一种无色透明液体,有氨味。该化合物在工业和研究中有一定的应用。
反式-4-[4-[[[5-[(3,4-二氟苯基)氨基]-1,3,4-恶二唑-2-基]羰基]氨基]苯基]环己烷乙酸(CAS号:892489-52-0)的物理化学性质是什么?
该化合物为白色固体,分子量为552.31 g/mol。它在水中溶解度较低,在有机溶剂如乙腈、乙酸乙酯中有较好的溶解性。该化合物具有较高的化学稳定性,对酸和碱具有...
如何处理含有Pyrotinib dimaleate(CAS号:1397922-61-0)的废料?
处理含有Pyrotinib dimaleate 的废料时,应遵循当地的法规要求。首先,收集废料并进行分类,确保没有与其他化学品混合。然后,采取适当的物理和化学处...
在合成中是否有4-(5-5-乙基-1,2,4-噁二唑-3-基)苯甲酸乙酯(CAS号:1166756-79-1)的替代品?
在合成过程中,可以考虑使用其他结构类似的化合物作为替代品,例如苯甲酸酯类化合物,如2-乙基-5-甲基噁二唑基苯甲酸乙酯等。这些替代品可能具有相似的化学性质,但在...
如何处理含有1-((叔丁氧基羰基)氨基)环丁烷甲酸甲酯(CAS号:880166-10-9)的废料?
处理含有该化合物的废液时,应先确保其完全反应并转化为无害物质。对于未反应的化合物,建议采用中和处理后进行蒸馏回收,剩余物可使用化学氧化法或焚烧法进行无害化处理。...
2-({[3,5-二(三氟甲基)苯基]磺酰基}氨基)-4-(甲基硫代)丁酸甲酯(CAS号:175202-21-8)的市场或研究趋势如何?
目前该化合物主要应用于药物合成领域,尤其在开发新型抗癌药物方面具有潜在应用。随着制药行业的持续发展,对于高效、低毒的合成中间体需求增加,预计该化合物的研究和应用...
N,N-乙烯双(碘乙酰胺)(CAS号:7250-43-3)的物理化学性质是什么?
N,N-乙烯双(碘乙酰胺)是一种白色或类白色固体,易溶于乙醇、丙酮等有机溶剂,但在水中溶解度较低。该化合物具有较高的反应活性,可以与其他含有活性氢的化合物发生酰...
7-Fluoro-1H-spiro[furo[3,4-c]pyridine-3,4'-piperidine](CAS号:1283090-73-2)通常如何合成?
该化合物可以通过环合反应合成,首先合成吡啶和哌啶的衍生物,然后在合适的条件下进行环合反应得到目标化合物。常用的催化剂包括某些金属盐类,产率一般在70%-90%之...
处理3-乙酰滇乌碱(CAS号:80787-51-5)时应注意哪些实验室安全事项?
在处理3-乙酰滇乌碱时,应穿戴适当的个人防护装备(PPE),如实验服、手套(丁腈手套或PVC手套)、护目镜和口罩。实验应在通风橱中进行,以减少吸入或皮肤接触的风...
如何储存2-溴-5-硝基-4-羧酸(CAS号:1053655-82-5)?
2-溴-5-硝基-4-羧酸应存放在阴凉、干燥、通风良好的地方,远离火源和热源。避免与还原剂、碱性物质接触。储存容器应密封,防止吸湿。
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.














![2-Methyl-2-propanyl [2-(2-oxa-6-azaspiro[3.3]hept-6-yl)ethyl]carbamate structure 2-Methyl-2-propanyl [2-(2-oxa-6-azaspiro[3.3]hept-6-yl)ethyl]carbamate structure](https://cnstatic.chemtradehub.com/structs/141/1415562-38-7-c0a4.webp)