Results 51 to 60 of about 7,932,784 (254)

A GENERAL PRESSURE TENSOR CALCULATION FOR MOLECULAR-DYNAMICS SIMULATIONS

, 1995
A hybrid method for the calculation of the pressure tenser in molecular dynamics (MD) simulations, which combines both the thermodynamic and mechanical definitions, is presented here.
BROWN, D,, NEYERTZ, S,
core   +5 more sources

Invisible but not inaccessible—Revealing transient oligomers formed by intrinsically disordered proteins with solution NMR and complementary methods

FEBS Letters, EarlyView.
Transient oligomers formed by intrinsically disordered proteins may be ‘invisible’ to direct detection yet remain accessible to solution NMR through equilibrium‐exchange measurements and pressure‐jump experiments. Complementary methods report on mass, stoichiometry, selected distance distributions, morphology, and internal packing.
Martin D. Gelenter, Ad Bax
wiley   +1 more source

Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database [PDF]

, 2007
Comparative molecular dynamics (MD) simulations enable us to explore the conformational dynamics of the active sites of distantly related enzymes.
Baaden, Marc, Muan Hong Ngd, Essex, Jonathan, Sansom, Mark, Cox, Katherine, Ng, Muan Hong, Tai, Kaihsu, Jonathan W. Essexc, Steven Johnstonc, Bing Wua, Marc Baadenb, Essex, Jonathan W., Sansom, Mark S.P., Murdock, Stuart, Wu, Bing, Stuart Murdockc, Johnston, Steven, Fangohr, Hans, Kaihsu Taia, Richard Boardmanc, Mark S. P. Sansoma, Katherine Coxa, Sansom, Mark S. P., Hans Fangohrd, Boardman, Richard   +24 more
core   +1 more source

Soft motions encoded by the fold and mediated by conserved hinge sites drive V‐ATPase allosteric machinery and autoinhibition

FEBS Letters, EarlyView.
Vacuolar H+‐ATPase (V‐ATPase) is a multisubunit rotary proton pump that acidifies intracellular compartments. Using elastic network models, we identified conserved hinge residues that govern its large‐scale functional motions. We show that intrinsically encoded ‘soft modes’ drive critical functional transitions, including rotary catalysis and ...
Diksha Parwana, Xiaowei Bogetti, Stuti Sharma, Ivet Bahar   +3 more
wiley   +1 more source

Towards improved simulations of self-organising molecular materials [PDF]

, 2009
Computer simulations can be used in parallel with experimental techniques to gain valuable insights into physical systems, test theoretical models or predict new be- haviour of molecular materials.
Lintuvuori, Juho Sakari, LINTUVUORI, JUHO,SAKARI   +1 more
core  

In vitro and in silico modelling of ROS1‐positive non‐small cell lung cancer reveals fusion‐dependent tyrosine kinase inhibitor responses

Molecular Oncology, EarlyView.
Drug resistance limits treatment success in a subset of lung cancers driven by ROS1 gene alterations. Using patient‐derived cells and computer simulations, we studied three key mutations and how they affect five targeted drugs. The mutations reduced drug effectiveness in different ways by altering protein structure and behavior.
Farhan Ul Haq, Marc Terrones, Felicia Rodrigues Fortes, Anne Schepers, Alessia Denis, Christophe Deben, Ken Op de Beeck, Guy Van Camp, Geert Vandeweyer   +8 more
wiley   +1 more source

The VHL tumor suppressor at the crossroad of protein folding, aggregation, and cancer

Molecular Oncology, EarlyView.
Mutations, environmental stress, and chaperone dysfunction can destabilize pVHL, promoting its conversion from the native folded state into amyloid‐like assemblies. This transition may contribute to protein storage, cell dormancy, survival, and drug resistance.
Lara Abad, Silvio Carlo Ermanno Tosatto, Emanuela Leonardi   +2 more
wiley   +1 more source

BioSimGrid: towards a worldwide repository for biomolecular simulations

, 2004
BioSimGrid is a database for biomolecular simulations, or, a 'Protein Data Bank extended in time' for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules.
Kaihsu Tai, Simon J. Cox, Jeffreys, Paul, Ng, Muan Hong, Tai, Kaihsu, Jonathan W. Essex, Muan Hong Ng, Mark S. P. Sansom, Stuart Murdock, Essex, Jonathan W., Sansom, Mark S.P., Murdock, Stuart, Steven Johnston, Wu, Bing, Hans Fangohr, Johnston, Steven, Fangohr, Hans, Sansom, Mark S. P., Bing Wu, Paul Jeffreys, Cox, Simon J.   +20 more
core   +1 more source

Mutant p53R273H disrupts PDPK1 homodimerization and contributes to PDPK1 activation

Molecular Oncology, EarlyView.
How mutant p53R273H drives AKT signaling is unclear. We show that p53R273H, but not wild‐type, directly binds PDPK1 via a mutation‐dependent conformational change. This interaction disrupts inhibitory PDPK1 homodimerization and enhances AKT phosphorylation.
Mei Chee Lim, Alvin Kunyao Guo, Yoko Itahana, Srinivasaraghavan Kannan, Valerie Goh, Mingmin Ong, Terina Yan Wen Tay, Weiying Ye, Sabhashina Radha Krishnan, Jun Nishiyama, Chandra S Verma, Koji Itahana   +11 more
wiley   +1 more source

Reprogramming tumor cells with LCOR mRNA nanotherapy to enhance immunotherapy

Molecular Oncology, EarlyView.
LCOR (Ligand‐dependent corepressor) mRNA encapsulated in polymeric nanoparticles restores LCOR activity in tumor cells, constraining aggressive tumor cell states and increasing tumor immunogenicity. This reprogramming makes tumor cells more vulnerable to T‐cell attack and enhances their response to immune‐checkpoint immunotherapy.
Gabriel Serra‐Mir, Elena Haro‐Martínez, Sandra Blasco‐Benito, Chiara Cannatà, José Ángel Palomeque, Anna López‐Plana, Maria Sanz‐Flores, Marc Sabartés, Cristina Fornaguera, Toni Celià‐Terrassa   +9 more
wiley   +1 more source