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Computational screening and molecular dynamic simulation of breast cancer associated deleterious non-synonymous single nucleotide polymorphisms in TP53 gene.

Chitrala KN, Yeguvapalli S - PLoS ONE (2014)

Bottom Line: Among them, TP53 is one of the major genetic risk factor which is known to be mutated in many of the breast tumor types.We have predicted three deleterious coding non-synonymous single nucleotide polymorphisms rs11540654 (R110P), rs17849781 (P278A) and rs28934874 (P151T) in TP53 with a phenotype in breast tumors using computational tools SIFT, Polyphen-2 and MutDB.We have performed molecular dynamics simulations to study the structural and dynamic effects of these TP53 mutations in comparison to the wild-type protein.

View Article: PubMed Central - PubMed

Affiliation: Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India.

ABSTRACT
Breast cancer is one of the most common cancers among the women around the world. Several genes are known to be responsible for conferring the susceptibility to breast cancer. Among them, TP53 is one of the major genetic risk factor which is known to be mutated in many of the breast tumor types. TP53 mutations in breast cancer are known to be related to a poor prognosis and chemo resistance. This renders them as a promising molecular target for the treatment of breast cancer. In this study, we present a computational based screening and molecular dynamic simulation of breast cancer associated deleterious non-synonymous single nucleotide polymorphisms in TP53. We have predicted three deleterious coding non-synonymous single nucleotide polymorphisms rs11540654 (R110P), rs17849781 (P278A) and rs28934874 (P151T) in TP53 with a phenotype in breast tumors using computational tools SIFT, Polyphen-2 and MutDB. We have performed molecular dynamics simulations to study the structural and dynamic effects of these TP53 mutations in comparison to the wild-type protein. Results from our simulations revealed a detailed consequence of the mutations on the p53 DNA-binding core domain that may provide insight for therapeutic approaches in breast cancer.

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Ligplot showing the interactions of metal ion (Zn) with the amino acid residues of the protein.An atom of Zn bound with a tetra-co-ordinate geometry to three Cysteines (Cys 176, 238 and 242) and one Histidine (His 179).
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pone-0104242-g001: Ligplot showing the interactions of metal ion (Zn) with the amino acid residues of the protein.An atom of Zn bound with a tetra-co-ordinate geometry to three Cysteines (Cys 176, 238 and 242) and one Histidine (His 179).

Mentions: To investigate the mechanism of structural consequences of the mutations on TP53 we performed molecular dynamics. Initial coordinates were extracted from the crystal structure of p53 core domain in the absence of DNA (PDB ID: 2ocj, chain A; resolution 2.05 A°) [21]. All water molecules were removed from the crystal structure and the mutants (MTs) R110P, P151T, P278A were created by replacing the wild-type (WT) protein residue with its polymorphic residue using PyMOL [22]. Molecular dynamic analysis was performed at 37°C (physiological temperature) and neutral pH using GROMACS 4.5.3 (http://www.gromacs.org/) [23]–[25]. The p53 core domain contains Zn2+ that is essential for activity. A LIGPLOT [26] scheme of Zn2+ interaction in the crystal structure of p53 core domain (PDB ID: 2ocj, chain A; resolution 2.05 A°) was shown in the Fig. 1 given below. Zn2+ remains bound to p53 core domain at temperatures below 30°C and it rapidly dissociates at physiological temperature such that a significant fraction appears in the apo state [27]. Consequently, we focused on both apo and holo simulations of wild (WT) and mutant type (MT) p53 core domain and presented here. The system was solvated by adding explicit flexible SPC water [28] embedded in a cubic box and the walls were located ≥10 Å from all protein atoms. Cl− counter ions (5, 3, 3, 5, 3, 5, 2 and 4 for holo WT, apo WT, apo P151T, holo P151T, apo P278A, holo P278A, apo R110P and holo R110P respectively) were added to neutralize the total charge of the system. The box size was set to 4.833 nm×4.027 nm×4.794 nm with box vectors 7.3 nm×7.3 nm×7.3 nm and box angles 900 for each side. Each solvated structure was energy minimized for 50000 steps of steepest descent minimization terminating when maximum force is found smaller than 1000 KJ/mol−1/nm−1. After energy minimization, the system was subject to equilibration at constant temperature (300K) and pressure (1 bar) with a time step of 2 fs and non bonded pair list updated every five steps under the conditions of position restraints for heavy atoms and LINCS constraints [29] for all bonds. The temperature was kept constant using a Berendsen thermostat [30]. Electrostatic interactions were calculated using the particle mesh Ewald summation method [31]. Finally, eight (i.e., apo WT, holo WT, apo R110P, holo R110P, apo P151T, holo P151T, apo P278A and holo P278A respectively) 10 ns Molecular dynamics simulations (MDS) were performed.


Computational screening and molecular dynamic simulation of breast cancer associated deleterious non-synonymous single nucleotide polymorphisms in TP53 gene.

Chitrala KN, Yeguvapalli S - PLoS ONE (2014)

Ligplot showing the interactions of metal ion (Zn) with the amino acid residues of the protein.An atom of Zn bound with a tetra-co-ordinate geometry to three Cysteines (Cys 176, 238 and 242) and one Histidine (His 179).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4126775&req=5

pone-0104242-g001: Ligplot showing the interactions of metal ion (Zn) with the amino acid residues of the protein.An atom of Zn bound with a tetra-co-ordinate geometry to three Cysteines (Cys 176, 238 and 242) and one Histidine (His 179).
Mentions: To investigate the mechanism of structural consequences of the mutations on TP53 we performed molecular dynamics. Initial coordinates were extracted from the crystal structure of p53 core domain in the absence of DNA (PDB ID: 2ocj, chain A; resolution 2.05 A°) [21]. All water molecules were removed from the crystal structure and the mutants (MTs) R110P, P151T, P278A were created by replacing the wild-type (WT) protein residue with its polymorphic residue using PyMOL [22]. Molecular dynamic analysis was performed at 37°C (physiological temperature) and neutral pH using GROMACS 4.5.3 (http://www.gromacs.org/) [23]–[25]. The p53 core domain contains Zn2+ that is essential for activity. A LIGPLOT [26] scheme of Zn2+ interaction in the crystal structure of p53 core domain (PDB ID: 2ocj, chain A; resolution 2.05 A°) was shown in the Fig. 1 given below. Zn2+ remains bound to p53 core domain at temperatures below 30°C and it rapidly dissociates at physiological temperature such that a significant fraction appears in the apo state [27]. Consequently, we focused on both apo and holo simulations of wild (WT) and mutant type (MT) p53 core domain and presented here. The system was solvated by adding explicit flexible SPC water [28] embedded in a cubic box and the walls were located ≥10 Å from all protein atoms. Cl− counter ions (5, 3, 3, 5, 3, 5, 2 and 4 for holo WT, apo WT, apo P151T, holo P151T, apo P278A, holo P278A, apo R110P and holo R110P respectively) were added to neutralize the total charge of the system. The box size was set to 4.833 nm×4.027 nm×4.794 nm with box vectors 7.3 nm×7.3 nm×7.3 nm and box angles 900 for each side. Each solvated structure was energy minimized for 50000 steps of steepest descent minimization terminating when maximum force is found smaller than 1000 KJ/mol−1/nm−1. After energy minimization, the system was subject to equilibration at constant temperature (300K) and pressure (1 bar) with a time step of 2 fs and non bonded pair list updated every five steps under the conditions of position restraints for heavy atoms and LINCS constraints [29] for all bonds. The temperature was kept constant using a Berendsen thermostat [30]. Electrostatic interactions were calculated using the particle mesh Ewald summation method [31]. Finally, eight (i.e., apo WT, holo WT, apo R110P, holo R110P, apo P151T, holo P151T, apo P278A and holo P278A respectively) 10 ns Molecular dynamics simulations (MDS) were performed.

Bottom Line: Among them, TP53 is one of the major genetic risk factor which is known to be mutated in many of the breast tumor types.We have predicted three deleterious coding non-synonymous single nucleotide polymorphisms rs11540654 (R110P), rs17849781 (P278A) and rs28934874 (P151T) in TP53 with a phenotype in breast tumors using computational tools SIFT, Polyphen-2 and MutDB.We have performed molecular dynamics simulations to study the structural and dynamic effects of these TP53 mutations in comparison to the wild-type protein.

View Article: PubMed Central - PubMed

Affiliation: Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India.

ABSTRACT
Breast cancer is one of the most common cancers among the women around the world. Several genes are known to be responsible for conferring the susceptibility to breast cancer. Among them, TP53 is one of the major genetic risk factor which is known to be mutated in many of the breast tumor types. TP53 mutations in breast cancer are known to be related to a poor prognosis and chemo resistance. This renders them as a promising molecular target for the treatment of breast cancer. In this study, we present a computational based screening and molecular dynamic simulation of breast cancer associated deleterious non-synonymous single nucleotide polymorphisms in TP53. We have predicted three deleterious coding non-synonymous single nucleotide polymorphisms rs11540654 (R110P), rs17849781 (P278A) and rs28934874 (P151T) in TP53 with a phenotype in breast tumors using computational tools SIFT, Polyphen-2 and MutDB. We have performed molecular dynamics simulations to study the structural and dynamic effects of these TP53 mutations in comparison to the wild-type protein. Results from our simulations revealed a detailed consequence of the mutations on the p53 DNA-binding core domain that may provide insight for therapeutic approaches in breast cancer.

Show MeSH
Related in: MedlinePlus