Protein simulations in confined environments

Research output: Contribution to journalConference article

Abstract

Materials surfaces mimic cell like architecture and proteins can be encapsulated by these material surfaces (e.g. a porous glass or gold). Depending on the number and types of surface interactions, this confine environment could destroy the protein or help it maintain its bioactivity. We developed computer models and simulation tools for the understanding of surface-protein interaction at the atomistic levels. At the molecular level, molecular dynamics simulations are very powerful, but the high computational cost of molecular simulations is a drawback. A viable alternative method to study protein-surface interactions is the coarse-grained molecular simulations of simplified models, such as elastic network model. At the atomic interaction level, we used ab initio simulations to calculate the potential between surface and protein atoms.

Original languageEnglish (US)
Article number14
Pages (from-to)133-137
Number of pages5
JournalProceedings of SPIE - The International Society for Optical Engineering
Volume5509
DOIs
StatePublished - Dec 1 2004

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Membrane Proteins
proteins
Proteins
Protein
Molecular Simulation
Simulation
simulation
surface reactions
Bioactivity
Interaction
Gold
Molecular dynamics
atomic interactions
Surface potential
Glass
Atoms
Computer simulation
Computer Model
Simulation Tool
Molecular Dynamics Simulation

All Science Journal Classification (ASJC) codes

  • Electrical and Electronic Engineering
  • Condensed Matter Physics

Cite this

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title = "Protein simulations in confined environments",
abstract = "Materials surfaces mimic cell like architecture and proteins can be encapsulated by these material surfaces (e.g. a porous glass or gold). Depending on the number and types of surface interactions, this confine environment could destroy the protein or help it maintain its bioactivity. We developed computer models and simulation tools for the understanding of surface-protein interaction at the atomistic levels. At the molecular level, molecular dynamics simulations are very powerful, but the high computational cost of molecular simulations is a drawback. A viable alternative method to study protein-surface interactions is the coarse-grained molecular simulations of simplified models, such as elastic network model. At the atomic interaction level, we used ab initio simulations to calculate the potential between surface and protein atoms.",
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Protein simulations in confined environments. / Cetinkaya, Murat; Sofo, Jorge Osvaldo; Demirel, Melik C.

In: Proceedings of SPIE - The International Society for Optical Engineering, Vol. 5509, 14, 01.12.2004, p. 133-137.

Research output: Contribution to journalConference article

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T1 - Protein simulations in confined environments

AU - Cetinkaya, Murat

AU - Sofo, Jorge Osvaldo

AU - Demirel, Melik C.

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AB - Materials surfaces mimic cell like architecture and proteins can be encapsulated by these material surfaces (e.g. a porous glass or gold). Depending on the number and types of surface interactions, this confine environment could destroy the protein or help it maintain its bioactivity. We developed computer models and simulation tools for the understanding of surface-protein interaction at the atomistic levels. At the molecular level, molecular dynamics simulations are very powerful, but the high computational cost of molecular simulations is a drawback. A viable alternative method to study protein-surface interactions is the coarse-grained molecular simulations of simplified models, such as elastic network model. At the atomic interaction level, we used ab initio simulations to calculate the potential between surface and protein atoms.

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