Molecular Dynamics And Its Effect On The Proteins Essay examples

Molecular Dynamics And Its Effect On The Proteins Essay examples

Length: 1414 words (4 double-spaced pages)

Rating: Better Essays

Open Document

Essay Preview

Molecular dynamics (MD) simulation was performed to investigate the site-specific glycosylation effect on the proteins. Model peptide system was galactosylated at different sites in silico, and the conformational characteristics of each glycosylate peptide were analyzed by the MD simulations. Only double-glycosylated peptide showed a structural disruption accompanying a helical splitting, in which Ser17 was particularly weak point to begin destabilization. The MD simulation revealed molecular-level mechanism of the glycosylation effect on the peptide to understand the experimentally observed phenomenon for inhibiting amyloid formation in the model peptide.

Keywords: Amyloid formation; Conformational analysis; Glycosylation; Molecular dynamics simulations; Partial charge; Sialic acid

Protein glycosylation is one of the most important forms of post-translational processing associated with numerous biological functions in life.1 Carbohydrates fulfill many common as well as extremely important functions in nature.2 Many reports claim that glycosylation changes structure, activity, and physical stability of proteins.2–4 Particularly for O-glycosylation, considerable evidence has been accumulated regarding cellular processes and human diseases.5,6 The conformational changes of protein structure are often related to neurodegenerative disorders such as Parkinson’s or Alzheimer’s disease.7,8 Site-specific O-glycosylation of tau protein is reported to be responsible for regulating protein aggregation.9 The O-glycosylation cycling also modulates tauopathy, amyloid β-peptide, and polyglutamine expansion in transgenic models.10 Molecular details played by glycosylation are complicated by the subtle nature of variations in the glycan structu...

... middle of paper ...

...ate gradient method to prepare the initial structure for MD simulations.

1.2 MD simulation and data analysis
The MD simulations were carried out using a sander module of Amber 12 program to trace the dynamic nature of each peptide with ff03 and GLYCAM force field. An implicit water model was used to treat the solvation effects with the modified Generalized Born/Surface Area (GB/SA) model developed by Onufriev and coworkers.16 Each peptide system was gradually heated to 298 K for 50 ps and equilibrated for 1 ns at the same temperature. A production MD run was performed for 200 ns with a time step of 1.0 fs, and the trajectory was collected for every 50 ps. A constant temperature of 298 K was regulated using a Langevin dynamics mode with 5.0 ps of collision frequency. The final MD trajectories were analyzed and processed using a ‘ptraj’ facility of the Amber program.

Need Writing Help?

Get feedback on grammar, clarity, concision and logic instantly.

Check your paper »

Essay about Visual Molecular Dynamics VMD

- VMD or Visual Molecular Dynamics is a computer program that can be used to design, animate, and model molecules especially organic molecules so that they can be visualized in 3-dimensional graphics for analysis and better understanding of their molecular structure and components. For the most part VMD is used to view and analyze the molecular stimulations, but the program also contains rendering tools that can be used to modify the dimensional and sequential data of the molecules. The data can be applied in various ways....   [tags: Computer Programs]

Free Essays
502 words (1.4 pages)

For Proteins, Form Shapes Function Essay

- Proteins are fundamental components of all living cells that participate in some of the most important biological processes, including cell growth and maintenance, movement and defense. They are complex molecules that consist of one or more chains of amino-acids, have distinct three-dimensional shapes and whose structure and structural dynamics directly influence their specific function. Most proteins have a primary, secondary and tertiary structure, but some of them, like hemoglobin, also have a quaternary structure....   [tags: Proteins, Structures, Functions]

Better Essays
1004 words (2.9 pages)

Essay on Dna Of Proteins : The Fish Muscle

- Analysis of proteins found in varying fish muscle Introduction Gel electrophoresis involves separation and analysis of macromolecules like deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and various proteins. In electrophoresis an electric current is passed through a solution or gel from one electrode to the other. Ions, molecules, and molecular fragments in the solution or gel are drawn to one of the electrodes according to their charge. When charged molecules are placed in a gel, the speed they travel toward the electrode is influenced by both their charge and size....   [tags: Protein, Molecular biology, Western blot]

Better Essays
984 words (2.8 pages)

Essay on Determination of Molecular Weight of a Protein by Gel Filtration

- Introduction Purification of proteins is an essential technique that provides biochemists with the ability to obtain a sample that contains a specific protein of interest. In order to purify a protein biochemists typically obtain the specific extract, precipitate the protein using ammonium sulfate, preform gel filtration, and lastly run ionic and affinity chromatography. Understanding the use and methods of the different chromatography techniques is of crucial importance in order to successfully purify and conclude the molecular weight of an unknown sample using elution volumes of molecular weight standards....   [tags: Determination of Molecular Weight]

Better Essays
2960 words (8.5 pages)

Essay on What is Molecular Biology?

- MOLECULAR BIOLOGY INTRODUCTION AND BACKGROUND INFORMATION Molecular biology is to characterize the structure, function and relationships between two types of macromolecules, DNA and proteins. This relatively limited definition will suffice to allow us to establish a date for the so-called "molecular revolution", or at least to establish a chronology of its most fundamental developments (Walker, 2009) .At the heart of this definition is the idea of the gene, this concept dates back to the decade of the 1860's....   [tags: macromolecules, DNA, proteins]

Better Essays
1731 words (4.9 pages)

A Study On Molecular Diagnostics Essay

- Chandni Shiwbodh Molecular Diagnostics Molecular Diagnostics is defined as tests which identify certain patterns in both RNA and DNA. These tests are able to identify RNA, genes, and protein sequences which play a role in diseases. These sequences may be linked to diseases which include nucleotide polymorphism, deletions, rearrangements, and many more. Molecular Diagnostics is also able to identify and multiply the presence of certain microorganisms and cells. Molecular Diagnostics provides a great amount of clinical information....   [tags: DNA, Mutation, Molecular biology]

Better Essays
1724 words (4.9 pages)

Molecular Biology And Expressing Gfp Essays

- November 14, 2016 Abigail Lammers Molecular Biology Marion Kawar Introduction: This lab dealt with molecular biology and expressing GFP in bacterial cells. Most of the lab dealt with plasmids. Plasmids are short, circular pieces of DNA that can be used to transmit genetic information into a host cell (for example: adding a gene that will make the host cell glow). These DNA pieces are separate from the rest of the genome and are replicated separately as well. Plasmids join to a DNA sequence through bacterial transformation....   [tags: DNA, Bacteria, Gene, Molecular biology]

Better Essays
2102 words (6 pages)

Cancer Cells and the Insulin-Growth Proteins Essay examples

- What if we use what our bodies already produce and use that to combat cancer. Proteins are large molecules that have multifunctional roles in our bodies. They are involved in almost all of our cell functions, like carrying and distributing oxygen throughout our bodies to creating our skin cells. They are the structure to all of our biological cells within all living things. A couple of scientists, from the Chinese University of Hong Kong, conducted several experiments manipulating and creating proteins to inhibit breast cancer cells and colon cancer cells from developing....   [tags: cancer, protein, hormone]

Better Essays
1006 words (2.9 pages)

Mitochondrial Protein Of Mitochondrial Proteins Essays

- The majority of mitochondrial proteins are encoded by the nuclear genome with only 13 polypeptides being encoded by mitochondrial genes which represent less than 1% of total mitochondrial protein. A prominent examples of mitochondrial proteins encoded by nuclear genome are FH and SDH enzyme complex which functions not only in mitochondrial energy production but also act as a tumor suppressors and mutations in both genes have been implicated in the predisposition to different type of cancer. (B. E....   [tags: Cancer, DNA, Mutation, Mitochondrion]

Better Essays
1262 words (3.6 pages)

Proteins Essay example

- Proteins Proteins are the macromolecules of life. Discovered in 1838, proteins are recognized as a large number of superior organic compounds that make up living organisms and are essential to their functioning. The term protein comes from the Greek word “proteies” or “primary”. Proteins have many different properties and function in a variety of ways. They can function as a building material, in teeth, bones and muscles, and they can serve as enzymes, hormones, and neurotransmitters. Its functions are the most diverse of any family....   [tags: science]

Better Essays
978 words (2.8 pages)