Moleculardynamics
Mostrando 1-12 de 29 artigos, teses e dissertações.
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1. Estudo dinâmico conformacional da proteína calgranulina C (S100A12) mediante interação com íons e receptor RAGE / Dynamic and conformational study of protein calgranulin C (S100A12) in interaction with ions and RAGE receptor
Calgranulina C (S100A12) é membro da família das proteínas S100 \"EF-hands\" que complexam cálcio. A S100A12 humana é expressa predominantemente por granulócitos e é superexpressa em compartimentos inflamatórios. Níveis séricos elevados de S100A12 são encontrados em pacientes acometidos por distúrbios inflamatórios, neurodegenerativos, metabóli
IBICT - Instituto Brasileiro de Informação em Ciência e Tecnologia. Publicado em: 03/05/2012
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2. Estudo atomístico da formação de interfaces orgânico-inorgânico: Tiofenos sobre óxido de titânio / Atomistic study of the formation of organic-inogarnic interfaces: thiophenes over titanium oxide
No estudo de sistemas híbridos orgânico-inorgânico, o uso de materiais como polímeros conjugados e óxidos de metal de transição tem despertado grande interes- se. Em particular, destacam-se sistemas compostos de tiofenos e óxido de titânio, que encontram uma importante aplicação em células solares. Para um melhor entendimento da interação entre
Publicado em: 2008
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3. Um potencial de interação para o estudo de materiais e simulações por dinâmica molecular
The Vashishta-Rahman effective interaction potential, based on the Pauling's concept of "ionic radii", has been successfully employed to investigate structural and dynamical properties of different classes of material. By celebrating Pauling's birth centenary, we review the building up of the Vashishta-Rahman potential and we present molecular-dynamics simul
Química Nova. Publicado em: 2001-12
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4. Arginine-Rich Peptides Destabilize the Plasma Membrane, Consistent with a Pore Formation Translocation Mechanism of Cell-Penetrating Peptides
Recent molecular-dynamics simulations have suggested that the arginine-rich HIV Tat peptides translocate by destabilizing and inducing transient pores in phospholipid bilayers. In this pathway for peptide translocation, Arg residues play a fundamental role not only in the binding of the peptide to the surface of the membrane, but also in the destabilization
The Biophysical Society.
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5. Water Replacement Hypothesis in Atomic Detail—Factors Determining the Structure of Dehydrated Bilayer Stacks
According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail.
The Biophysical Society.
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6. Peptide Nanopores and Lipid Bilayers: Interactions by Coarse-Grained Molecular-Dynamics Simulations
A set of 49 protein nanopore-lipid bilayer systems was explored by means of coarse-grained molecular-dynamics simulations to study the interactions between nanopores and the lipid bilayers in which they are embedded. The seven nanopore species investigated represent the two main structural classes of membrane proteins (α-helical and β-barrel), and the seve
The Biophysical Society.
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7. Subpicosecond conformational dynamics of small peptides probed by two-dimensional vibrational spectroscopy
The observation of subpicosecond fluctuations in the conformation of a small peptide in water is demonstrated. We use an experimental method that is specifically sensitive to conformational dynamics taking place on an ultrafast time scale. Complementary molecular-dynamics simulations confirm that the conformational fluctuations exhibit a subpicosecond c
The National Academy of Sciences.
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8. Molecular-Dynamics Simulations of ELIC—a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor
The ligand-gated ion channel from Erwinia chrysanthemi (ELIC) is a prokaryotic homolog of the eukaryotic nicotinic acetylcholine receptor (nAChR) that responds to the binding of neurotransmitter acetylcholine and mediates fast signal transmission. ELIC is similar to the nAChR in its primary sequence and overall subunit organization, but despite their structu
The Biophysical Society.
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9. Interactions of H562 in the S5 Helix with T618 and S621 in the Pore Helix Are Important Determinants of hERG1 Potassium Channel Structure and Function
hERG1 is a member of the cyclic nucleotide binding domain family of K+ channels. Alignment of cyclic nucleotide binding domain channels revealed an evolutionary conserved sequence HwX(A/G)C in the S5 domain. We reasoned that histidine 562 in hERG1 could play an important structure-function role. To explore this role, we created in silica models of the hERG1
The Biophysical Society.
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10. High-Chloride Concentrations Abolish the Binding of Adenine Nucleotides in the Mitochondrial ADP/ATP Carrier Family
The ADP/ATP carrier (AAC) is a very effective membrane protein that mediates the exchange of ADP and ATP across the mitochondrial membrane. In vivo transport measurements on the AAC overexpressed in Escherichia coli demonstrate that this process can be severely inhibited by high-chloride concentrations. Molecular-dynamics simulations reveal a strong modific
The Biophysical Society.
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11. Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data
Force-field validation is essential for the identification of weaknesses in current models and the development of more accurate models of biomolecules. NMR coupling and relaxation methods have been used to effectively diagnose the strengths and weaknesses of many existing force fields. Studies using the ff99SB force field have shown excellent agreement betwe
The Biophysical Society.
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12. Molecular Determinants of Snurportin 1 Ligand Affinity and Structural Response upon Binding
The transport of large biomolecules such as proteins and RNA across nuclear pore complexes is a field of strong interest and research. Although the basic mechanisms are fairly well understood, the details of the underlying intermolecular interaction within these transport complexes are still unclear. The recognition dynamics and energetics of cargo binding t
The Biophysical Society.