Computer-aided Target Analysis for Mutagenesis

Experimental studies of mutations in proteins are expensive and time-consuming, and thus the number of mutants included in such studies is limited. In contrast, computational mutagenesis analysis can be performed on a large number of mutants, and with efficient algorithms and software, all possible mutants of a given protein can be analyzed. Creative Biolabs is dedicated to establishing the most exquisite service platform for our clients and our one-stop protein engineering services can provide comprehensively technical support to advance our clients’ projects.

Molecular Dynamics for Mutagenesis

Molecular dynamics of complex biological and chemical systems is possible using personal computers due to increased computer performance and improved software design. Molecular dynamics equilibrations are used to provide a means for measuring structural fluctuations. These fluctuations assist in defining a distance coordinate, or reaction coordinate, that is relevant to the function of the protein. In addition, molecular dynamics are demonstrated to evaluate the energy landscape, or potential of mean force, along with the chosen reaction coordinate. The potential of mean force identifies variations of the predominant structures among mutants that may affect the function.

The structural effects of mutations on proteins are analyzed by using molecular dynamics methods that are Not Another Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) programs. For protein systems of approximately 15-200 amino acids, one can obtain details about structural and functional changes related to mutations in a timeframe of 1 week to 1 year. The actual timescale depends on the computer, size of the molecular system, and the number of molecular system variations being studied.

An in silico method for the site-specific mutation to standard and phosphorylated amino acids was described below.

a) Save a clean pdb
b) Generating a protein structure file
c) Mutating the protein
d) Mutating to phosphorylated amino acids
e) Solvating the protein
f) Molecular dynamics
g) Distance measurement
h) Adaptive biasing force (abf) simulations
i) Data analysis

Fig.1 The structure of the tryptophan zipper with PDB ID 1LE0.

Services

In silico methods have increasingly been valuable and popular in molecular biology, for mutagenesis analysis to account for the function of a particular amino acid in a protein mutant. In most molecular dynamics software, standard and phosphorylated amino acids can be substituted site-specifically. Multiple mutations can be made by sequential mutagenesis within the software. Mutated molecules can be subsequently simulated using a few different strategies. Therefore, we can provide various molecular dynamics services such as NAMD and VMD to meet customers’ specific requirements.

Creative Biolabs has focused on the development of protein engineering for years. We whole-heartedly cooperate with you to accomplish our shared goals. Our team provides you with outstanding support and meets your specific needs with a professional technology platform. If you are interested in our services, please contact us for more details.

All listed services and products are For Research Use Only. Do Not use in any diagnostic or therapeutic applications.

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