Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics

2015 ◽  
Vol 119 (41) ◽  
pp. 12963-12969 ◽  
Author(s):  
Ivan Gladich ◽  
Alex Rodriguez ◽  
Rolando P. Hong Enriquez ◽  
Filomena Guida ◽  
Federico Berti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Organic Molecules ◽  
High Affinity ◽  
Explicit Solvent

scholarly journals Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics and Monte Carlo Approach

2013 ◽  
Vol 104 (2) ◽  
pp. 556a
Author(s):  
Rolando P. Hong Enriquez ◽  
Silvia Pavan ◽  
Fabio Benedetti ◽  
Alessandro Tossi ◽  
Adriano Savoini ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Organic Molecules ◽  
Short Peptides ◽  
Monte Carlo Approach ◽  
High Affinity

Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach

2012 ◽  
Vol 8 (3) ◽  
pp. 1121-1128 ◽  
Author(s):  
Rolando P. Hong Enriquez ◽  
Silvia Pavan ◽  
Fabio Benedetti ◽  
Alessandro Tossi ◽  
Adriano Savoini ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Organic Molecules ◽  
Short Peptides ◽  
Monte Carlo Approach ◽  
High Affinity

A MOLECULAR DYNAMICS STUDY OF ELECTRONIC SPUTTERING OF LARGE ORGANIC MOLECULES

1989 ◽  
Vol 50 (C2) ◽  
pp. C2-33-C2-35 ◽  
Author(s):  
D. FENYÖ ◽  
B. U.R. SUNDQVIST ◽  
B. KARLSSON ◽  
R. E. JOHNSON
Keyword(s):  
Molecular Dynamics ◽  
Organic Molecules

scholarly journals Computational Design of Macrocyclic Binders of S100B(ββ): Novel Peptide Theranostics

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 721
Author(s):  
Srinivasaraghavan Kannan ◽  
Pietro G. A. Aronica ◽  
Thanh Binh Nguyen ◽  
Jianguo Li ◽  
Chandra S. Verma
Keyword(s):  
Molecular Dynamics ◽  
Computational Design ◽  
Diagnostic Tools ◽  
Stapled Peptides ◽  
Altered Expression ◽  
Cellular Processes ◽  
High Affinity ◽  
Limited Success ◽  
Dynamics Simulations ◽  
Partner Proteins

S100B(ββ) proteins are a family of multifunctional proteins that are present in several tissues and regulate a wide variety of cellular processes. Their altered expression levels have been associated with several human diseases, such as cancer, inflammatory disorders and neurodegenerative conditions, and hence are of interest as a therapeutic target and a biomarker. Small molecule inhibitors of S100B(ββ) have achieved limited success. Guided by the wealth of available experimental structures of S100B(ββ) in complex with diverse peptides from various protein interacting partners, we combine comparative structural analysis and molecular dynamics simulations to design a series of peptides and their analogues (stapled) as S100B(ββ) binders. The stapled peptides were subject to in silico mutagenesis experiments, resulting in optimized analogues that are predicted to bind to S100B(ββ) with high affinity, and were also modified with imaging agents to serve as diagnostic tools. These stapled peptides can serve as theranostics, which can be used to not only diagnose the levels of S100B(ββ) but also to disrupt the interactions of S100B(ββ) with partner proteins which drive disease progression, thus serving as novel therapeutics.

scholarly journals Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

2014 ◽  
Vol 82 (7) ◽  
pp. 1319-1331 ◽  
Author(s):  
Garrett B. Goh ◽  
Benjamin S. Hulbert ◽  
Huiqing Zhou ◽  
Charles L. Brooks
Keyword(s):  
Molecular Dynamics ◽  
Constant Ph ◽  
Explicit Solvent ◽  
Constant Ph Molecular Dynamics

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

2016 ◽  
Vol 18 (18) ◽  
pp. 13052-13065 ◽  
Author(s):  
Emanuel K. Peter ◽  
Joan-Emma Shea ◽  
Igor V. Pivkin
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein Folding ◽  
Kinetic Monte Carlo ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Accelerated Simulation ◽  
Explicit Solvent ◽  
Exchange Algorithms

In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC).

Exploring the binding mechanism of positive allosteric modulators in human metabotropic glutamate receptor 2 using molecular dynamics simulations

2021 ◽  
Author(s):  
Panpan Wang ◽  
Xiaonan Gao ◽  
Ke Zhang ◽  
Qinglan Pei ◽  
Xiaobo Xu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Glutamate Receptor ◽  
Metabotropic Glutamate Receptor ◽  
Binding Mode ◽  
Allosteric Modulators ◽  
Binding Mechanism ◽  
Metabotropic Glutamate ◽  
High Affinity ◽  
Dynamics Simulations ◽  
High Electronegativity

Based on the binding mode and electrostatics, the features of high affinity PAMs were the reduced hydrophobicity with low electronegativity of R1, increased hydrophobicity with low electronegativity of R2 and with high electronegativity of linker.

scholarly journals Formation of complex organic molecules in ice mantles: An ab initio molecular dynamics study

2019 ◽  
Vol 629 ◽  
pp. A28 ◽  
Author(s):  
Natalia Inostroza ◽  
Diego Mardones ◽  
Jose Cernicharo ◽  
Hans Zinnecker ◽  
Jixing Ge ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Organic Molecules ◽  
Closed Shell ◽  
Ab Initio Molecular Dynamics ◽  
Young Stellar Objects ◽  
Stellar Objects ◽  
Detailed Simulation ◽  
Dust Grain ◽  
Complex Organic

We present a detailed simulation of a dust grain covered by a decamer of (CH3OH)10-ice-mantle, bombarded by an OH− closed-shell molecule with kinetic energies from 10–22 eV. The chemical pathways are studied through Born-Oppenheimer (ab initio) molecular dynamics. The simulations show that methanol ice-mantles can be a key generator of complex organic molecules (COMs). We report the formation of COMs such as methylene glycol (CH2(OH)2) and the OCH2OH radical, which have not been detected yet in the interstellar medium (ISM). We discuss the chemical formation of new species through the reaction of CH3OH with the hydroxyl projectile. The dependence of the outcome on the kinetic energy of the projectile and the implications for the observation and detection of these molecules might explain why the methoxy radical (CH3  ⋅ ) has been observed in a wider range of astrophysical environments than the hydroxymethyl (CH2OH ⋅) isomer. Because of the projectile kinetic energies required for these reactions to occur, we suggest that these processes are likely relevant in the production of COMs in photodissociation and shock regions produced by high-velocity jets and outflows from young stellar objects.

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