DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol

Smith, Nicholas; Witham, Shawn; Sarkar, Subhra; Zhang, Jie; Li, Lin; Li, Chuan; Alexov, Emil

doi:10.1093/bioinformatics/bts200

Cited by 46 publications

(45 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, each PDB file was split by chain designator and three files were generated: two files containing the atomic coordinates of each monomer and another file that contains the entire homodimeric structure. DelPhi [37,38,39] was run on each of these three files, and from the output the location of the geometric center for each monomer and the locations of the centers of positive and negative charges for the homodimer were determined. These runs were conducted using Clemson University’s High Performance Computing cluster, Palmetto (http://citi.clemson.edu/palmetto/).…”

Section: Methodsmentioning

confidence: 99%

On the electrostatic properties of homodimeric proteins

Campbell

Petukh

Alexov

et al. 2014

J. Theor. Comput. Chem.

Self Cite

View full text Add to dashboard Cite

A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology, 9(2), e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily in an electrostatic funnel. It is demonstrated that the electrostatic dipole moment of the dimer is predominantly perpendicular to the axis connecting the centers of the mass of the monomers. In addition, the surface points with highest potential are located in the proximity of the interfacial plane of the homodimeric complexes. These findings indicate that frequently homodimerization provides specific electrostatic features needed for the function of proteins.

show abstract

Section: Methodsmentioning

confidence: 99%

On the electrostatic properties of homodimeric proteins

Campbell

Petukh

Alexov

et al. 2014

J. Theor. Comput. Chem.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The molecular dynamic simulation was performed to calculate the total energy difference in solvated condition using the Poisson-Boltzmann equation (PBE) solver online tool (Smith et al, 2012;Sarkar et al, 2013). The simulation was performed by placing the protein under these conditions: i) interior dielectric constant: 4.00, ii) exterior dielectric constant: 80.00, iii) percentage fill: 80, grid scale: 2.00, iv) salt concentration: 0.10, v) probe radius: 1.40, and vi) boundary conditions: 2.00.…”

Section: Methodsmentioning

confidence: 99%

Modelling functional and structural impact of non-synonymous single nucleotide polymorphisms of the DQA1 gene of three Nigerian goat breeds

Yakubu¹,

Donato²,

Imumorin³

2017

SA J. An. Sci.

View full text Add to dashboard Cite

The DQA1 gene is a member of the highly polymorphic MHC class II locus that is responsible for the differences among individuals in immune response to infectious agents. In this study, the authors performed a comprehensive computational analysis of the functional and structural impact of non-synonymous or amino acid-changing single nucleotide polymorphisms (SNPs) (nsSNPs) that are deleterious to the DQA1 protein in Nigerian goats. A 310-bp fragment of exon 2 of the DQA1 gene was amplified and sequenced in 27 unrelated animals that are representative of three major Nigerian goat breeds (nine each of West African Dwarf, Red Sokoto, and Sahel of both sexes) using genomic DNA. Forty-two nsSNPs were identified from the alignment of the deduced amino acid sequences. Based on the PANTHER, PROVEAN and PolyPhen-2 algorithms, there was consensus in identifying the mutants I26D, E114V and V115F as being deleterious. Further, differences between the native and the mutant proteins in the subsequent molecular trajectory analysis (stabilizing and flexible residue composition, total grid energy, solvation energy, coulombic energy, solvent accessibility, and protein-protein interaction properties) revealed E114V and V115F to be highly deleterious. Combined mutational analysis comparing the amutant (I26D, E114V and V115F mutations collectively) with the native protein also showed changes that could affect protein function and structure. Further wet-lab confirmatory analysis in a pathological association study involving a larger population of goats is required at the DQA1 locus. This would lay a sound foundation for breeding disease-resistant individuals in the future. ______________________________________________________________________________________

show abstract

“…For example, the "finite element method", (Davis and McCammon 1990;Project 1995;Harvey 1989;Orttung 1977;Terán et al 1989) the "finite difference method", (Davis and McCammon 1990;Project 1995;Harvey 1989;Warwicker and Watson 1982;Holst 1993;Davis et al 1991;Sakalli and Knapp 2015) and the "boundary element method" (Davis and McCammon 1990;Project 1995;Harvey 1989;Juffer 1993Juffer , 1998Juffer et al 1991) are applied to solve the PB equation for biomolecular systems. There are also a number of generalized program packages available to study biomolecular phenomena (Warwicker and Watson 1982;Holst 1993;Davis et al 1991;Bashford and Gerwert 1992;Honig and Nicholls 1995;Juffer 1992) and web-servers (Calixto 2010;Anandakrishnan et al 2012;Smith et al 2012;Wang et al 2016). A quite recent new numerical implementation is the Gaussian-based dielectric function description for the nonlinear PB (NLPB) .…”

Section: A Thermodynamical Picturementioning

confidence: 99%

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

daSilva

Dias

2017

Biophys Rev

View full text Add to dashboard Cite

pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-ofthe-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.

show abstract

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol

Cited by 46 publications

References 10 publications

On the electrostatic properties of homodimeric proteins

On the electrostatic properties of homodimeric proteins

Modelling functional and structural impact of non-synonymous single nucleotide polymorphisms of the DQA1 gene of three Nigerian goat breeds

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

Contact Info

Product

Resources

About