Limits...
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.

Show MeSH

Related in: MedlinePlus

Propensity of cavity-lining atoms to occur in different secondary structural elements. Percentage compositions used in the calculation of propensities are available in Supplementary Figure S5c and d.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2724294&req=5

Figure 6: Propensity of cavity-lining atoms to occur in different secondary structural elements. Percentage compositions used in the calculation of propensities are available in Supplementary Figure S5c and d.

Mentions: The propensities of different secondary structural elements to be associated with cavities are shown in Figure 6. The significance of the propensity values has been confirmed from the z-values (38), shown in Supplementary Figure S6a. In PD cavities, strands are the most preferred element, followed by helices, as has been observed in protein–protein interfaces (10). However, in PR cavities, the helices are the only preferred element. The involvement of strand residues in PD cavities can be seen in Supplementary Figure S7a.Figure 6.


Cavities in protein-DNA and protein-RNA interfaces.

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

Propensity of cavity-lining atoms to occur in different secondary structural elements. Percentage compositions used in the calculation of propensities are available in Supplementary Figure S5c and d.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: Propensity of cavity-lining atoms to occur in different secondary structural elements. Percentage compositions used in the calculation of propensities are available in Supplementary Figure S5c and d.
Mentions: The propensities of different secondary structural elements to be associated with cavities are shown in Figure 6. The significance of the propensity values has been confirmed from the z-values (38), shown in Supplementary Figure S6a. In PD cavities, strands are the most preferred element, followed by helices, as has been observed in protein–protein interfaces (10). However, in PR cavities, the helices are the only preferred element. The involvement of strand residues in PD cavities can be seen in Supplementary Figure S7a.Figure 6.

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