Molecular dynamics simulation

In this Masters thesis computational modelling techniques were employed to investigate iron-free apo-Lactoferrin (apo-Lf) structural conformation changes in the presence of variant temperature and pH. These conditions represent the environment most milk protein goes through in food processing and the production of food products.

162p runthenight04 02-02-2023 9 3   Download

The thesis is structured as follows: In Chapter 1, the scientific literature is summarized within the scope of this study. Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study. Chapter 3 identifies the important residues of the LsIA/α7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. The effects of C-terminal modification of LsIA on interactions with α3β2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4.

234p runthenight04 02-02-2023 11 3   Download

In this paper a molecular dynamics simulation of nano-metric cutting of copper with a diamond tool is presented. MD simulations require the determination of the interaction of the involved atoms through a function of potential for the materials involved in the analysis and the accurate topography of the studied area, leading to high demand of computational time.

12p tohitohi 19-05-2020 29 1   Download

In  Molecular simulation of nanoparticle diffusion at fluid interfaces molecular dynamics simulations are used to exam- ine the transport properties of a nanoparticle in both bulk solvent and at a liquid–liquid interface. Specifically it aims to address the effect of interfacial adsorption on the diffusion of nanoparticles (at low concentration).

5p hoquangbio 22-07-2015 30 3   Download

Retinol-binding protein transports retinol, and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic con-ditions retinol-binding protein undergoes a transition to the molten globule state, and releases the bound retinol ligand. A biased molecular dynamics simulation method has been used to generate models for the ensemble of conformers populated within this molten globule state.

13p fptmusic 12-04-2013 42 3   Download

The low affinity of peptide nucleic acid (PNA) to hybridize with DNA in the presence of a mismatch endows PNA with a high degree of discriminat-ory capacity that has been exploited in therapeutics for the selective inhibi-tion of the expression of point-mutated genes. To obtain a structural basis for this intriguing property, molecular dynamics simulations are carried out on PNAÆDNA duplexes formed at the Ki-ras proto-oncogene, compri-sing the point-mutated (GAT), and the corresponding wild-type (GGT) codon 12. ...

16p fptmusic 11-04-2013 55 2   Download

The NMR solution structures of NTX-1 (PDB code 1W6B and BMRB 6288), a long neurotoxin isolated from the venom ofNaja naja oxiana, and the molecular dynamics simulation of these structures are reported. Calculations are based on 1114NOEs, 19 hydrogen bonds, 19 dihedral angle restraints and secondary chemical shifts derived from 1 Hto 13 C HSQC spectrum. Similar to other long neurotoxins, the three-finger like structure shows a double and a triple strandedb-sheet aswell as some flexible regions, particularly at the tip of loop II and the C-terminal tail....

0p awards 05-04-2013 49 2   Download

Experimental autoimmune encephalomyelitis can be induced in susceptible animals by immunodominant deter-minants of myelin basic protein (MBP). To characterize the molecular features of antigenic sites important for designing experimental autoimmune encephalomyelitis suppressing molecules, we report structural studies, based on NMR experimental data in conjunction with molecular dynamic simulations, of the potent linear dodecapeptide epitope of guinea pig MBP, Gln74-Lys75-Ser76-Gln77-Arg78-Ser79-Gln80-Asp81-Glu82-Asn83-Pro84-Val85 [MBP(74–85)], and its antagonist analogue Ala81MBP(74–85)....

15p awards 05-04-2013 56 3   Download

A comprehensive study of the hydration mechanism of an enzyme in non-aqueous media was done using molecular dynamics simulations in five organic solvents with different polarities, namely, hexane, 3-pentanone, diisopropyl ether, ethanol, and acetonitrile.

13p galaxyss3 19-03-2013 61 4   Download

Molecular dynamics simulations employing a combined quantum mechani-cal and molecular mechanical potential have been carried out to elucidate the reaction mechanism of the hydrolysis of a cyclic nucleotide cAMP sub-strate by phosphodiesterase 4B (PDE4B).

17p cosis54 05-01-2013 45 4   Download

Prediction and understanding of the folding and stability of the 3D struc-ture of proteins is still a challenge. The different atomic interactions, such as non polar contacts and hydrogen bonding, are known but their exact relative weights and roles when contributing to protein folding and stability are not identified.

17p cosis54 08-12-2012 43 2   Download

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học quốc tế cung cấp cho các bạn kiến thức về ngành y đề tài: High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study

5p toshiba17 31-10-2011 53 2   Download