#VMD MEASURE MEAN SQUARE DISPLACEMENT FREE#

Neighbour (KNN), and Random Forest to forecast Sequences and adjusted parameters, we utilized support vector machines (SVM), With Turi Create applied, we trained the data and got the predicted 9 MnP PLMC module analysis and the distance matrix of amino acid

#VMD MEASURE MEAN SQUARE DISPLACEMENT FREE#

The single point free energy produced by FoldX. Based on the MnP sequenceīLAST, we did 16 cores calculation in parallel, and the results were essentially Matrix of amino acid residues between proteins ( Fig. We wrote PLMC module to explore the ectopic dominance of mutated MnP, and to plot 8 SASA trend of the wtMnP in the dynamic simulation. The internal structure at higher temperatures.įig. However as the subsequent temperature continued to rise, the area of SASA would decrease instead. It was possible that the enzyme activity would decrease in this temperature range, but the number of binding sites would increase. While the average value of SASA reached the highest value around 45℃-65℃ (seen in Parts ). The solvent accessible surface area is larger, which is more conducive to the related docking of the Value and trend of SASA were more obvious as the temperature rised. Therefore as we simulated the temperature around the protein ( Fig. Solvent accessibility surface area (SASA) usually reflects the relevant sites whereĬan bind. 7 Hydrogen Bonds of MnP in the dynamic simulation E. Protein to change, the number of hydrogen bonds decreased, and theįig. With the change of temperature, the structure of MnP and theĮxistence of hydrogen bonds will change as well.Īs can be seen from the picture below, the high temperature above 120 ℃ caused the structure Protein hydrogen bonding is a very important non-covalent structural force, and anįactor affecting protein stability. We could be found from the figure that as the temperature increased, the curve describing the radius of gyration (unit: Å) shifted upward and the amplitude increased, suggesting that at high temperatures, the protein structure will become looser and it is difficult to have a stable conformation.įig. The smaller the value, the greater the compactness of MnP, and the greater the expansion of Over time, the radius of gyration is a physical quantity that describes the compactness of the Gyrates show the variation of the radius of gyration of protein ( R g R_g R g ) 5 MnP secondary structure changes with temperature. Three indices reflected the disruption of protein structural stability caused byįig. 5), and the number of salt bridges increased with the rise of In our simulation, the shrinkingīesides, secondary structure numbers decreased, β-sheetĭamaged ( Fig. 4), which represented the disruption ofįig. The white area shown in the dynamic Ramachandran plot we obtained shrank Ramachandran plot is a way to visualize energetically allowed regions for backbone dihedral anglesĪgainst φ of amino acid residues in protein structure, and thus reflects the secondary This curve interfaces with every residueįig.

Sensitive to temperature, thus facilitating the later construction of a single mutation library.Ĭompared the RMSF library curve with the B-factor plotįrom the R package Bio3d, and the filtrated range of residues was almost the same.This indicates that when protein crystals are heated by X-ray irradiation, our model is consistent with the actual thermal movement level of amino acid residues.įig. Under four reaction temperatures, and it revealed that mainly No. Through the analysis of the track file of MD simulation, we obtained the RMSF plot ( Fig. This reference position willīased on the RMSF curve acquired from classic MD simulations, we could measure the sensitivity of Is the reference position of particle i i i. Reference structure, r r e f r_ RMSF i = ⎣ ⎡ T 1 t j = 1 ∑ T ∣ ∣ r i ( t j ) − r i ref ∣ ∣ 2 ⎦ ⎤ 1/2 (usually the backbone atoms) of superimposed proteins. Root-mean-square deviation (RMSD) is the measure of the average distance between the Simulations for a better understanding of the protein characteristics. Protein secondary structure, and salt bridge number of MnP. High-precision 3D structure and the potential to degrade PE, we must obtain the details of theĪchieve this goal, molecular dynamic (MD) simulations were utilized to analyze the stability, To obtain a sound analysis of our key function enzyme, manganese peroxidase (MnP, PDB code: 3M5Q),

Vmd measure mean square displacement