Molecular dynamics simulations on constraint metal binding peptides

Kantarci, Nigar; Tamerler, Candan; Sarıkaya, Mehmet; Haliloğlu, Türkan; Doruker, Pemra

doi:10.1016/j.polymer.2005.03.016

Cited by 50 publications

(36 citation statements)

References 16 publications

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“…6(b)). The -OH group in strong binder lies relatively closer with the metal surface [16], which can also be observed in Fig. 5(c).…”

Section: Static Propertiessupporting

confidence: 68%

“…By MD methods, Braun et al [15] simulated multi-peptides interacting with gold of 5 ns. Similarly, Kantarci et al [16] carried out explicit solvent MD simulations on four different peptide sequences in the absence and presence of the metal surface and analyzed the relationship between sequence, structure and binding process for metal binding peptides.…”

Section: Introductionmentioning

confidence: 99%

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Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Yang

Zhao

2007

Engineering Analysis with Boundary Elements

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Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and Au the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. r

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“…6(b)). The -OH group in strong binder lies relatively closer with the metal surface [16], which can also be observed in Fig. 5(c).…”

Section: Static Propertiessupporting

confidence: 68%

Section: Introductionmentioning

confidence: 99%

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Yang

Zhao

2007

Engineering Analysis with Boundary Elements

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“…For platinum, molecular dynamics simulations of strong and weak Pt-binding peptides indicate that strong binders frequently contain the structural motif TST. 18 Although both threonine and serine bind strongly to gold surfaces as homopolypeptides, neither shows a similar affinity for platinum. 11 Because TST is the most flexible region of the peptides in their study and appears frequently in Pt-binding peptides, the authors suggested that the motif's flexibility is important for the peptide's affinity for platinum.…”

Section: Introductionmentioning

confidence: 99%

Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations

2009

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We report all-atom molecular dynamics simulations following adsorption of gold-binding and non-gold-binding peptides on gold surfaces modeled with dispersive interactions. We examine the dependence of adsorption on both identity of the amino acids and mobility of the peptides. Within the limitations of the approach, results indicate that when the peptides are solvated, adsorption requires both configurational changes and local flexibility of individual amino acids. This is achieved when peptides consist mostly of random coils or when their secondary structural motifs (helices, sheets) are short and connected by flexible hinges. In the absence of solvent, only affinity for the surface is required: mobility is not important. In combination, these results suggest the barrier to adsorption presented by displacement of water molecules requires conformational sampling enabled through mobility.

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“…Sóvágó and Ősz (2006) reported that glutamic acid and aspartic acid have negatively charged from carboxyl groups that can bind with positive ions of iron. Cates et al (2002) and Kantarcia et al (2005) reported that serine and threonine have negatively charged from the hydroxyl group that can bind with positive ions of iron. Lee et al (2009) reported that lysine also has a high affinity for metal.…”

Section: Resultsmentioning

confidence: 99%

The Effect of Ascorbic Acid and Soybean Protein Hyrolysate to Iron Binding Capacity

Wijayanti

Maryana

Susanti

et al. 2020

crbb

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The study aimed to investigate the effect of ascorbic acid and soybean protein hydrolysate to iron-binding capacity. BPPT (Agency for the Assessment and Application of Technology) developed soybean hydrolysate, which was obtained by thermal and enzymatic hydrolysis. Ascorbic acid was added in sample preparation with composition 0, 50, 75 and 100%. Soybean protein hydrolysate (SPH) was prepared by gel filtration chromatography using Sephadex G-25 to separate peptide based on molecular weight. Characterization of SPH and SPH fractions was also conducted, such as protein concentration, molecular weight, iron-binding capacity, and amino acid concentration. Iron binding capacity was determined by the colorimetric method using an ortho-phenanthroline reagent. The result showed that soybean protein hydrolysate increases iron-binding capacity 25-37 times than ascorbic acid. Arginine, aspartic acid, glutamic acid, threonine, lysine, and serine were found as amino acids responsible for iron-binding capacity in the SPH.

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Molecular dynamics simulations on constraint metal binding peptides

Cited by 50 publications

References 16 publications

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations

The Effect of Ascorbic Acid and Soybean Protein Hyrolysate to Iron Binding Capacity

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