Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin
Literature Information
Manoj Mandal, Chaitali Mukhopadhyay
An all atom molecular dynamics simulation was used to explore the atomic detail mechanism of guanidinium induced unfolding of the protein ubiquitin. Ubiquitin unfolds through pre-unfolded (intermediate) states, i.e. guanidinium induced unfolding of ubiquitin appears to be a multi-step process, and loss of hydrophobic contacts of C-terminal residues is crucial for ubiquitin unfolding. Free-energy landscapes show that barrier separation between folded and unfolded basins is ∼5.0 kcal mol−1, and both the basins are of comparable energy. It was observed that guanidinium ions interact directly with ubiquitin. Favorable electrostatic interaction is the main driving force for such accumulation of guanidinium ions near protein, but van der Waals energy also contributes. RDF plots show that accumulation of guanidinium ions near specific residues is the main cause for destabilization of intra-residue interactions crucial to maintain the three-dimensional fold of the protein. One salt-bridge interaction between Lys11 and Glu34 appears to be important to maintain the crystal structure of ubiquitin and this salt-bridge can map the unfolding process of ubiquitin.
Recommended Journals
Related Literature
Chemical profiling of cerebrospinal fluid by multiple reaction monitoring mass spectrometry‡
Christina R. Ferreira, Karen E. Yannell, Brit Mollenhauer, Ryan D. Espy, Fernanda B. Cordeiro, Z. Ouyang, R. G. Cooks
DOI: 10.1039/C6AN01618A
An electrochemical biosensor for rapid detection of E. coli O157:H7 with highly efficient bi-functional glucose oxidase-polydopamine nanocomposites and Prussian blue modified screen-printed interdigitated electrodes
Meng Xu, Ronghui Wang
DOI: 10.1039/C6AN00873A
SERS detection of uranyl using functionalized gold nanostars promoted by nanoparticle shape and size
Grace Lu, Tori Z. Forbes, Amanda J. Haes
DOI: 10.1039/C6AN00891G
High throughput LSPR and SERS analysis of aminoglycoside antibiotics
Kristy S. McKeating, Maxime Couture, Marie-Pier Dinel, Sylvie Garneau-Tsodikova, Jean-Francois Masson
DOI: 10.1039/C6AN00540C
Nanoporous gold leaf as a signal amplification agent for the detection of VOCs with a quartz crystal microbalance
Lu Zhang, Yuan Liu, Han Song, Bintong Huang
DOI: 10.1039/C6AN00556J
Dyneon THV, a fluorinated thermoplastic as a novel material for microchip capillary electrophoresis
Nacéra Aboud, Davide Ferraro, Myriam Taverna, Stéphanie Descroix, Claire Smadja, N. Thuy Tran
DOI: 10.1039/C6AN00821F
Fluorescence suppression using micro-scale spatially offset Raman spectroscopy
Claudia Conti, Alessandra Botteon, Chiara Colombo, Marco Realini, Pavel Matousek
DOI: 10.1039/C6AN00852F
Nanoscale silicon surface-assisted laser desorption/ionization mass spectrometry: environment stability and activation by simple vacuum oven desiccation
Chia-Wen Tsao, Yuan-Jing Lin, Pi-Yu Chen, Yu-Liang Yang, Say Hwa Tan
DOI: 10.1039/C6AN00659K
Multiplexed cancer biomarker detection using chip-integrated silicon photonic sensor arrays
Adam L. Washburn, Winnie W. Shia, Kimberly A. Lenkeit, So-Hyun Lee, Ryan C. Bailey
DOI: 10.1039/C6AN01076H
Investigating non-specific binding to chemically engineered sensor surfaces using liposomes as models
C. Fenzl, C. Genslein, C. Domonkos, K. A. Edwards, T. Hirsch
DOI: 10.1039/C6AN00820H
You might also like
What precautions should be taken when handling 2-Chloro-1,2-bis(4-methylphenyl)ethanone (CAS: 71193-32-3)?
When handling 2-Chloro-1,2-bis(4-methylphenyl)ethanone (CAS: 71193-32-3), it is ...
What industries use 4-Ethoxy-3-(5-methyl-4-oxo-7-propyl-1,4-dihydroimidazo[5,1-f][1,2,4]triazin-2-yl)benzenesulfonyl chloride (CAS: 224789-26-8)?
4-Ethoxy-3-(5-methyl-4-oxo-7-propyl-1,4-dihydroimidazo[5,1-f][1,2,4]triazin-2-yl...
How should Methyl 3-Oxo-4-Androsten-17-Carboxylate (CAS: 2681-55-2) be stored?
Methyl 3-Oxo-4-Androsten-17-Carboxylate (CAS: 2681-55-2) should be stored in a c...
What are the main uses of (R)-3-Amino-4-(3-hexylphenylamino)-4-oxobutylphosphonic acid (CAS: 909725-61-7)?
(R)-3-Amino-4-(3-hexylphenylamino)-4-oxobutylphosphonic acid is primarily used i...
What regulatory guidelines apply to 2-Methyl-2-propanyl 3-amino-3-carbamoyl-1-azetidinecarboxylate (CAS: 1254120-14-3)?
2-Methyl-2-propanyl 3-amino-3-carbamoyl-1-azetidinecarboxylate (CAS: 1254120-14-...
Are there alternatives to (E)-4-(tert-Butoxy)-4-oxobut-2-enoic acid (CAS: 135355-96-3) in synthesis?
There are alternative reagents that can be used in synthesis instead of (E)-4-(t...
What are the physical and chemical properties of [2-(3-Chlorophenyl)-1,3-thiazol-4-yl]methanol (CAS: 121202-20-8)?
[2-(3-Chlorophenyl)-1,3-thiazol-4-yl]methanol (CAS: 121202-20-8) is a crystallin...
What is the market or research trend for Methyl (2S)-[(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]{[(4-methylphenyl)sulfonyl]oxy}acetate (CAS: 166249-17-8)?
The market and research trends for Methyl (2S)-[(4S)-2,2-dimethyl-1,3-dioxolan-4...
What is the market or research trend for 1-Bromo-2-isocyanatoethane (CAS: 42865-19-0)?
The market for 1-Bromo-2-isocyanatoethane (CAS: 42865-19-0) is driven by its use...
What are the main uses of 4-Nitro-D-phenylalanine hydrochloride (CAS: 147065-06-3)?
4-Nitro-D-phenylalanine hydrochloride (CAS: 147065-06-3) is primarily used in re...
Source Journal
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.












![6-[2-(Trifluoromethoxy)phenyl]-2-pyridinecarboxylic acid structure 6-[2-(Trifluoromethoxy)phenyl]-2-pyridinecarboxylic acid structure](https://static.chemtradehub.com/structs/887/887983-48-4-f6ac.webp)
![6-Nitro-2-(4-nitrophenyl)imidazo[1,2-a]pyridine structure 6-Nitro-2-(4-nitrophenyl)imidazo[1,2-a]pyridine structure](https://static.chemtradehub.com/structs/118/118000-57-0-cb82.webp)
