Limits...
ProteinVolume: calculating molecular van der Waals and void volumes in proteins.

Chen CR, Makhatadze GI - BMC Bioinformatics (2015)

Bottom Line: Quantitative understanding of these effects is important for predicting and designing proteins with predefined response to changes in hydrostatic pressure using computational approaches.The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for separate calculations.ProteinVolume is a highly accurate and fast application to interrogate geometric volumes of proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, 12180, USA. chenc13@rpi.edu.

ABSTRACT

Background: Voids and cavities in the native protein structure determine the pressure unfolding of proteins. In addition, the volume changes due to the interaction of newly exposed atoms with solvent upon protein unfolding also contribute to the pressure unfolding of proteins. Quantitative understanding of these effects is important for predicting and designing proteins with predefined response to changes in hydrostatic pressure using computational approaches. The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for separate calculations.

Results: We developed ProteinVolume, a highly robust and easy-to-use tool to compute geometric volumes of proteins. ProteinVolume generates the molecular surface of a protein and uses an innovative flood-fill algorithm to calculate the individual components of the molecular surface volume, van der Waals and intramolecular void volumes. ProteinVolume is user friendly and is available as a web-server or a platform-independent command-line version.

Conclusions: ProteinVolume is a highly accurate and fast application to interrogate geometric volumes of proteins. ProteinVolume is a free web server available on http://gmlab.bio.rpi.edu . Free-standing platform-independent Java-based ProteinVolume executable is also freely available at this web site.

Show MeSH

Related in: MedlinePlus

Schematic diagram depicting surface and volume definitions. The solvent accessible surface is made by tracing out the center of solvent probes (blue circles) rolled around the entire protein surface. The molecular surface definition cleanly separates geometric or solvent-excluded volume (VSE) from the envelope volume (VE) reflecting to solute-solvent interactions. The molecular surface volume (VMS) is the sum of the van der Waals (VVDW) and void volumes (VVoid).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4379742&req=5

Fig1: Schematic diagram depicting surface and volume definitions. The solvent accessible surface is made by tracing out the center of solvent probes (blue circles) rolled around the entire protein surface. The molecular surface definition cleanly separates geometric or solvent-excluded volume (VSE) from the envelope volume (VE) reflecting to solute-solvent interactions. The molecular surface volume (VMS) is the sum of the van der Waals (VVDW) and void volumes (VVoid).

Mentions: The volume that a protein occupies in solution is an important thermodynamic parameter: the change in protein volume upon unfolding defines the changes in stability as a function of pressure, ΔV = (∂ΔG/∂P)T. Experimental studies have shown that such changes upon unfolding of proteins are small and range from −4.0 to +1.0% [1-3]. The volume of a protein in solution can be divided into its protein-solvent interaction volume and geometric volume. The protein-solvent interaction volume is affected by the hydrophobicity, polarity, and charge distribution of surface residues of the protein. The geometric volume is the solvent-excluded volume, which is enclosed within the solvent-excluded surface (Figure 1). The solvent-excluded surface was termed the molecular surface by Richards in 1977 [4]. In this paper, we will refer to the solvent-excluded volume as the molecular surface volume (VMS). The molecular surface volume comprises of the intrinsic volume of protein atoms termed van der Waals volume (VVDW), and the intramolecular void volume (VVoid) that arises due to imperfect packing between protein atoms (Figure 1). The solvent accessible surface is the surface delineated by the center of a solvent probe rolling around the protein. The volume enclosed by this surface is termed the solvent accessible volume (VSA). The volume enclosed between the solvent accessible surface and molecular surface is the envelope volume (VE = VSA - VMS). It is well established that the voids in the native protein structure determine the pressure unfolding of proteins [5,6]. In this paper, we will focus on the calculation of the geometric volume of a protein enclosed within the molecular surface, which can be computed knowing the Cartesian coordinates of protein atoms found in PDB structure files.Figure 1


ProteinVolume: calculating molecular van der Waals and void volumes in proteins.

Chen CR, Makhatadze GI - BMC Bioinformatics (2015)

Schematic diagram depicting surface and volume definitions. The solvent accessible surface is made by tracing out the center of solvent probes (blue circles) rolled around the entire protein surface. The molecular surface definition cleanly separates geometric or solvent-excluded volume (VSE) from the envelope volume (VE) reflecting to solute-solvent interactions. The molecular surface volume (VMS) is the sum of the van der Waals (VVDW) and void volumes (VVoid).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4379742&req=5

Fig1: Schematic diagram depicting surface and volume definitions. The solvent accessible surface is made by tracing out the center of solvent probes (blue circles) rolled around the entire protein surface. The molecular surface definition cleanly separates geometric or solvent-excluded volume (VSE) from the envelope volume (VE) reflecting to solute-solvent interactions. The molecular surface volume (VMS) is the sum of the van der Waals (VVDW) and void volumes (VVoid).
Mentions: The volume that a protein occupies in solution is an important thermodynamic parameter: the change in protein volume upon unfolding defines the changes in stability as a function of pressure, ΔV = (∂ΔG/∂P)T. Experimental studies have shown that such changes upon unfolding of proteins are small and range from −4.0 to +1.0% [1-3]. The volume of a protein in solution can be divided into its protein-solvent interaction volume and geometric volume. The protein-solvent interaction volume is affected by the hydrophobicity, polarity, and charge distribution of surface residues of the protein. The geometric volume is the solvent-excluded volume, which is enclosed within the solvent-excluded surface (Figure 1). The solvent-excluded surface was termed the molecular surface by Richards in 1977 [4]. In this paper, we will refer to the solvent-excluded volume as the molecular surface volume (VMS). The molecular surface volume comprises of the intrinsic volume of protein atoms termed van der Waals volume (VVDW), and the intramolecular void volume (VVoid) that arises due to imperfect packing between protein atoms (Figure 1). The solvent accessible surface is the surface delineated by the center of a solvent probe rolling around the protein. The volume enclosed by this surface is termed the solvent accessible volume (VSA). The volume enclosed between the solvent accessible surface and molecular surface is the envelope volume (VE = VSA - VMS). It is well established that the voids in the native protein structure determine the pressure unfolding of proteins [5,6]. In this paper, we will focus on the calculation of the geometric volume of a protein enclosed within the molecular surface, which can be computed knowing the Cartesian coordinates of protein atoms found in PDB structure files.Figure 1

Bottom Line: Quantitative understanding of these effects is important for predicting and designing proteins with predefined response to changes in hydrostatic pressure using computational approaches.The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for separate calculations.ProteinVolume is a highly accurate and fast application to interrogate geometric volumes of proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, 12180, USA. chenc13@rpi.edu.

ABSTRACT

Background: Voids and cavities in the native protein structure determine the pressure unfolding of proteins. In addition, the volume changes due to the interaction of newly exposed atoms with solvent upon protein unfolding also contribute to the pressure unfolding of proteins. Quantitative understanding of these effects is important for predicting and designing proteins with predefined response to changes in hydrostatic pressure using computational approaches. The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for separate calculations.

Results: We developed ProteinVolume, a highly robust and easy-to-use tool to compute geometric volumes of proteins. ProteinVolume generates the molecular surface of a protein and uses an innovative flood-fill algorithm to calculate the individual components of the molecular surface volume, van der Waals and intramolecular void volumes. ProteinVolume is user friendly and is available as a web-server or a platform-independent command-line version.

Conclusions: ProteinVolume is a highly accurate and fast application to interrogate geometric volumes of proteins. ProteinVolume is a free web server available on http://gmlab.bio.rpi.edu . Free-standing platform-independent Java-based ProteinVolume executable is also freely available at this web site.

Show MeSH
Related in: MedlinePlus