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Cavities in protein-DNA and protein-RNA interfaces.

Sonavane S, Chakrabarti P - Nucleic Acids Res. (2009)

Bottom Line: A parameter, cavity index, measuring the degree of surface complementarity, indicates that the packing of atoms in protein-protein/DNA/RNA is very similar, but it is about two times less efficient in the permanent interfaces formed between subunits in homodimers.As within the tertiary structure and protein-protein interfaces, protein-DNA interfaces have a higher inclination to be lined by beta-sheet residues; from the DNA side, base atoms, in particular those in minor grooves, have a higher tendency to be located in cavities.A small fraction of water molecules are found to mediate hydrogen-bond interactions with both the components, suggesting their primary role is to fill in the void left due to the local non-complementary nature of the surface patches.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India.

ABSTRACT
An analysis of cavities present in protein-DNA and protein-RNA complexes is presented. In terms of the number of cavities and their total volume, the interfaces formed in these complexes are akin to those in transient protein-protein heterocomplexes. With homodimeric proteins protein-DNA interfaces may contain cavities involving both the protein subunits and DNA, and these are more than twice as large as cavities involving a single protein subunit and DNA. A parameter, cavity index, measuring the degree of surface complementarity, indicates that the packing of atoms in protein-protein/DNA/RNA is very similar, but it is about two times less efficient in the permanent interfaces formed between subunits in homodimers. As within the tertiary structure and protein-protein interfaces, protein-DNA interfaces have a higher inclination to be lined by beta-sheet residues; from the DNA side, base atoms, in particular those in minor grooves, have a higher tendency to be located in cavities. The larger cavities tend to be less spherical and solvated. A small fraction of water molecules are found to mediate hydrogen-bond interactions with both the components, suggesting their primary role is to fill in the void left due to the local non-complementary nature of the surface patches.

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Related in: MedlinePlus

Surface representation of the cavities present at protein–DNA interface. Two types of cavities possible at the interface involving a homodimeric protein are shown using the structure of EBNA-1 Nuclear protein–DNA complex (PDB file, 1b3t); protein and DNA chains are displayed in cartoon.
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Figure 1: Surface representation of the cavities present at protein–DNA interface. Two types of cavities possible at the interface involving a homodimeric protein are shown using the structure of EBNA-1 Nuclear protein–DNA complex (PDB file, 1b3t); protein and DNA chains are displayed in cartoon.

Mentions: To be compatible with our earlier analysis (10) cavities were identified using the CASTp (Computed Atlas of Surface Topography of proteins) server (33) located at http://sts.bioengr.uic.edu/castp/, with the default probe radius of 1.4 Å. Cavity classes considered in this analysis are designated as (i) PD (in the interface formed by a protein subunit and DNA), (ii) PDP (located between DNA and both the subunits of homodimeric proteins) and (iii) PR (in monomeric protein–RNA interface). The first two are illustrated in Figure 1. To be considered as an interface cavity it should have at least 20% of the cavity-lining atoms from both DNA and the protein component. For homodimeric proteins if both the subunits contribute to the cavity it is identified as PDP. Only the cavities with volume >11.5 Å3 (the volume of the probe with radius 1.4 Å) were included in the analysis. For the identification of water molecules structures determined to a resolution of 2.4 Å or better were used (25) and the PD and PR cavities were classified as solvated or empty based on the presence or the absence of crystallographically determined water molecules in them. Hydrogen bonds involving the water molecule (to protein atoms, as well as to other water molecules in the cavity) were determined using HBPLUS (34). The molecular diagrams were made using MSMS (35) and VMD (36).Figure 1.


Cavities in protein-DNA and protein-RNA interfaces.

Sonavane S, Chakrabarti P - Nucleic Acids Res. (2009)

Surface representation of the cavities present at protein–DNA interface. Two types of cavities possible at the interface involving a homodimeric protein are shown using the structure of EBNA-1 Nuclear protein–DNA complex (PDB file, 1b3t); protein and DNA chains are displayed in cartoon.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2724294&req=5

Figure 1: Surface representation of the cavities present at protein–DNA interface. Two types of cavities possible at the interface involving a homodimeric protein are shown using the structure of EBNA-1 Nuclear protein–DNA complex (PDB file, 1b3t); protein and DNA chains are displayed in cartoon.
Mentions: To be compatible with our earlier analysis (10) cavities were identified using the CASTp (Computed Atlas of Surface Topography of proteins) server (33) located at http://sts.bioengr.uic.edu/castp/, with the default probe radius of 1.4 Å. Cavity classes considered in this analysis are designated as (i) PD (in the interface formed by a protein subunit and DNA), (ii) PDP (located between DNA and both the subunits of homodimeric proteins) and (iii) PR (in monomeric protein–RNA interface). The first two are illustrated in Figure 1. To be considered as an interface cavity it should have at least 20% of the cavity-lining atoms from both DNA and the protein component. For homodimeric proteins if both the subunits contribute to the cavity it is identified as PDP. Only the cavities with volume >11.5 Å3 (the volume of the probe with radius 1.4 Å) were included in the analysis. For the identification of water molecules structures determined to a resolution of 2.4 Å or better were used (25) and the PD and PR cavities were classified as solvated or empty based on the presence or the absence of crystallographically determined water molecules in them. Hydrogen bonds involving the water molecule (to protein atoms, as well as to other water molecules in the cavity) were determined using HBPLUS (34). The molecular diagrams were made using MSMS (35) and VMD (36).Figure 1.

Bottom Line: A parameter, cavity index, measuring the degree of surface complementarity, indicates that the packing of atoms in protein-protein/DNA/RNA is very similar, but it is about two times less efficient in the permanent interfaces formed between subunits in homodimers.As within the tertiary structure and protein-protein interfaces, protein-DNA interfaces have a higher inclination to be lined by beta-sheet residues; from the DNA side, base atoms, in particular those in minor grooves, have a higher tendency to be located in cavities.A small fraction of water molecules are found to mediate hydrogen-bond interactions with both the components, suggesting their primary role is to fill in the void left due to the local non-complementary nature of the surface patches.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India.

ABSTRACT
An analysis of cavities present in protein-DNA and protein-RNA complexes is presented. In terms of the number of cavities and their total volume, the interfaces formed in these complexes are akin to those in transient protein-protein heterocomplexes. With homodimeric proteins protein-DNA interfaces may contain cavities involving both the protein subunits and DNA, and these are more than twice as large as cavities involving a single protein subunit and DNA. A parameter, cavity index, measuring the degree of surface complementarity, indicates that the packing of atoms in protein-protein/DNA/RNA is very similar, but it is about two times less efficient in the permanent interfaces formed between subunits in homodimers. As within the tertiary structure and protein-protein interfaces, protein-DNA interfaces have a higher inclination to be lined by beta-sheet residues; from the DNA side, base atoms, in particular those in minor grooves, have a higher tendency to be located in cavities. The larger cavities tend to be less spherical and solvated. A small fraction of water molecules are found to mediate hydrogen-bond interactions with both the components, suggesting their primary role is to fill in the void left due to the local non-complementary nature of the surface patches.

Show MeSH
Related in: MedlinePlus