ALANINE SCANING OF PROTEIN TRAF2

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ALANINE SCANING OF PROTEIN TRAF2 IN STRUCTURE OF THE COMPLEX BETWEEN THE N-TERMINAL DOMAIN OF TRADD AND THE TRAF DOMAIN OF TRAF2

Order alaning scaning

We perform an alanine scaning of protein TRAF2 during the formation of a dimeric complex TRADD-TRAF 2 (PDB:1F3V). In the protein TRAF2, the listed amino acid residues will be replaced by alainin while alaning scaning

protein TRAF2 during the formation of a dimeric complex TRADD-TRAF 2 (PDB:1F3V)

List 1 of substitutions of amino acid residues in a protein  TRAF2 while alaning scaning

467468469470471472473474475476
SERGLYCYSPROLEUPHECYSPROVALSER

List 2 of substitutions of amino acid residues in a protein TRAF2

400 401 402 403
GLYTHRGLYARG

The results obtained by alaning scaning for proteins with a known three-dimensional structure :

1.Determination of the stability of protein complexes 

with point substitutions of amino acid residues taking into account the three-dimensional structure of the biocomplex, based on the introduced criterion: the condition number of pairwise potential energy of electrostatic interaction of amino acid residues.

2.The range of changes in the affinity of the dimeric complex

 will be obtained at each substitution. The biophysical approach developed in the article allows one to qualitatively determine key amino acid residues when interacting two polypeptide chains, as well as to estimate the range of Kd change when replacing key amino acid residues in peptides when they are bound to the target protein. Thus, we can predict the stability of protein complexes. Also we can predict qualitatively determine the dissociation constant. We can synthesize peptides with a given dissociation constant to various proteins, while allowing to increase the selectivity of peptides. Increasing affinity for one protein and decreasing to others, which is an important condition for improving peptide therapy.

3. The potential energy values 

of the potential energy of the interaction between all amino acid residues of one protein and amino acid residues of another protein at each substitution

4. Differential Entropy Change

 Differential Entropy Change Values for Each Change. When inserted amino acid residue in a hydrophobic pocket consisting of other amino acid residues inside the pocket with the great probability to stay amino acid residue, which has a change in entropy (H, where H is entropy), as well as the difference between the mean square deviation (√D, where D is variance) for this replacement amino acid residue and standard deviation amino acid residue of wild type protein in a hydrophobic pocket will be minimal. It should be noted that √D correlates with lg(cond(W)), which in this formulation of the problem characterizes the stability of the biological complex.

5. The value lg(cond(w)) at each replacement.

The stability criterion of the protein complex (lg(cond(W)) of pairwise electrostatic interaction of the potential energy of amino acid residues allows us to estimate the range of variation of Kd values and indicate which mutations in peptides will lead to an increase/decrease in the stability of the biological complex when they are bound to proteins. Thus, before conducting a costly, time-consuming experiment, when it is necessary to synthesize a highly selective peptide, which will be characterized by high affinity for one protein and low affinity for another protein, then the method developed by us will minimize the number of experiments to search for such a peptide by theoretical calculation of a given range for high and low Kd values.

Three-dimensional graph 

6.Three-dimensional graph of the potential energy of electrostatic interaction between two wild-types proteins. Maps of potential energy of electrostatic interaction of amino acid residues of proteins involved, which allow visualizing the nature of the formation of a protein complex, identifying the maxima and minima of potential energy between amino acid residues of two proteins and identifying key amino acid residues that account for the maximum values of potential energy. Particular attention is paid to the nature of the interacting amino acid residues (hydrophobic, hydrophilic, charged). The analysis of interacting proteins was carried out taking into account the three-dimensional structure.

The customers can make their wishes and changes to the order.The customer will receive a graphical representation of the change in the range of affinity for the subsequent substitution of amino acid residues for alanine.

The order price depends on the applied calculation accuracy: 85% or 89%

Alanine scan with 85% computational accuracy —716 Euro. All materials will be provided after 10 business days after 100% payment

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Alanine scan with 89% computational accuracy —1190 Euro. All materials will be provided after 15 business days after 100% payment


You can also get right now the results of numerical calculations

You can also get right now the results of numerical calculations on the basis of the energy-calculated interaction between wild-type proteins TRADD-TRAF2 . These tables indicates the key energy interactions, important amino acid residues, potential energy values, as well as amino acid residues that account for the largest and lowest interaction values. Amino acid residues with high potential energy values can contribute to the entropy of a biological complex

the energy-calculated interaction between wild-type proteins TRADD-TRAF2
The table of values of the potential energy of electrostatic interaction between two wt proteins TRADD-TRAF2 (PDB:1F3V) (59 Euro)

with high potential energy values can contribute to the entropy of a biological complex
A plot of a three-dimensional map of the potential energy of interaction between two wild-type proteins TRADD-TRAF2 (PDB:1F3V) (112 EURO)

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