How Charged Amino Acids Regulate Nucleation of Biomimetic Hydroxyapatite Nanoparticles on the Surface of Collagen Mimetic Peptides: Molecular Dynamics and Free Energy Investigations

2020 ◽  
Vol 20 (7) ◽  
pp. 4561-4572
Author(s):  
Xiaohui Tan ◽  
Zhiyu Xue ◽  
Hua Zhu ◽  
Xin Wang ◽  
Dingguo Xu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Free Energy ◽  
Hydroxyapatite Nanoparticles ◽  
Charged Amino Acids ◽  
Mimetic Peptides ◽  
Collagen Mimetic Peptides ◽  
Biomimetic Hydroxyapatite

Evaluation of Deformation Mechanisms at Mineral-Protein Composite Interface Using Steered Molecular Dynamics Simulations

2004 ◽  
Vol 844 ◽  
Author(s):  
Dinesh R. Katti ◽  
Pijush Ghosh ◽  
Kalpana Katti
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Steered Molecular Dynamics ◽  
Clay Nanocomposites ◽  
Strain Behavior ◽  
New Class ◽  
Charged Amino Acids ◽  
Tension And Compression ◽  
Dynamics Simulations

AbstractIn the area of clay-polymer nanocomposites, recently montmorillonite is extensively used because of its unique characteristics of swelling. In this work, steered molecular dynamics is used to evaluate the mechanical behavior of a new class of nanocomposites, using amino acids to intercalate clay interlayers. Two positively charged amino acids, lysine and arginine, are used here. Our simulation indicates that both the amino acids have preferred orientation inside the clay interlayer. Our simulations also indicate that the clay-amino acid interlayer is about three times stiffer under tension as compared to under compression. On the other hand, dry montmorillonite shows similar stiffness under tension and compression. The fundamental mechanism of deformation during tension and compression is intrinsically different in the amino acid-clay composite. The stress-strain behavior of this clay-amino acid interlayer is predominantly linear until a stress of 1.5 GPa. This study is a first step towards the potential use of biomacromolecules as modifiers in clay nanocomposites.

scholarly journals Improved Sampling in Ab Initio Free Energy Calculations of Biomolecules at Solid–Liquid Interfaces: Tight-Binding Assessment of Charged Amino Acids on TiO2 Anatase (101)

Computation ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 12 ◽  
Author(s):  
Lorenzo Agosta ◽  
Erik G. Brandt ◽  
Alexander Lyubartsev
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Ab Initio ◽  
Tight Binding ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Ab Initio Simulations ◽  
Adsorption Free Energy ◽  
Charged Amino Acids ◽  
Solid Liquid

Atomistic simulations can complement the scarce experimental data on free energies of molecules at bio-inorganic interfaces. In molecular simulations, adsorption free energy landscapes are efficiently explored with advanced sampling methods, but classical dynamics is unable to capture charge transfer and polarization at the solid–liquid interface. Ab initio simulations do not suffer from this flaw, but only at the expense of an overwhelming computational cost. Here, we introduce a protocol for adsorption free energy calculations that improves sampling on the timescales relevant to ab initio simulations. As a case study, we calculate adsorption free energies of the charged amino acids Lysine and Aspartate on the fully hydrated anatase (101) TiO2 surface using tight-binding forces. We find that the first-principle description of the system significantly contributes to the adsorption free energies, which is overlooked by calculations with previous methods.

Mechanical Behavior of Collagen Mimetic Peptides Under Fraying Deformation via Molecular Dynamics

2019 ◽  
Author(s):  
Atul Rawal ◽  
Kristen L. Rhinehardt ◽  
Ram V. Mohan
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Mechanical Behavior ◽  
Cell Attachment ◽  
Alpha Helix ◽  
Sequence Length ◽  
Collagen Peptides ◽  
Mimetic Peptides ◽  
Collagen Mimetic Peptides ◽  
Helical Protein

Abstract Collagen is a pervasive, triple helical, extracellular matrix (ECM) protein, found in human body from skin and bones to blood vessels and lungs, making it biocompatible, biodegradable, capable of cell attachment, and relevant for applications in bio-polymers, tissue engineering and a plethora of other bio-medical fields. Natural collagen’s extraction from natural sources is time consuming, sometimes costly, and it is difficult to render, and could present undesired biological and pathogenic changes. Nanoscale collagen mimetic peptides (Synthetic Collagen), without the unwanted biological entities present in the medium, has shown to mimic the unique properties that are present in natural collagen. Synthetic collagen, thus provides a superior alternative compared to natural collagen for its utilization in several applications. Their properties are affected by surrounding environments, including various solvents, and can be tailored toward specific applications. The focus of this paper is to investigate the mechanical properties of these nanoscale collagen mimetic peptides with lengths of about 10nm, leading to understanding of their feasibility in bio-printing of a composite polymeric collagen biomaterial with a blend of multiple synthetic collagen molecules. Molecular dynamics modeling is used to simulate, model and analyze mechanical properties of synthetic collagen peptides. In particular, mechanical behavior of these peptides are studied. An in-depth insight into the deformation and structural properties of the collagen peptides are of innovative significance for a multitude of bio medical engineering applications. Present paper employed steered molecular dynamics as the principal method of investigating the mechanical properties of nanoscale collagen mimetic peptide 1BKV, which closely resembles natural collagen with a shorter sequence length of 30 amino acids. A detailed comprehension of the protein’s mechanical properties is investigated through fraying deformation behavior studied. A calculated Gibbs free energy value of 40 Kcal/mol corresponds with a complete unfolding of a single alpha-helix peptide chain from a triple helical protein in case of fraying. Force needed for complete separation of the alpha-helix from the triple-helical protein is analyzed, and discussed in this paper.

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