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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

The largest PDP cavity located in 1mdy (volume 828 Å3, Rvs 0.59 and 9 water molecules).
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Figure 3: The largest PDP cavity located in 1mdy (volume 828 Å3, Rvs 0.59 and 9 water molecules).

Mentions: The total volume of the cavities in individual interface is poorly correlated with the interface size (defined by number of atoms present in the interface) (Supplementary Figure S1), as was observed in protein–protein interfaces. However, for individual cavities one can use power law or linear fit (Supplementary Table S4) to express the variation of the volume with the number of atoms or residues lining the cavity (Supplementary Figure S2). Typical of tertiary structure cavities (10), approximately five atoms or four cavity-lining residues are needed to accommodate one water molecule. The distribution of volumes of cavities is shown in Figure 2a. Like the cavities in protein–protein interfaces, protein–nucleic-acid interfaces also contain higher percentage of cavities that are larger than 100 Å3—7.2 and 6.5% for PD and PR cavities, relative to 2.6% in cavities in the tertiary structure. However, the PDP cavities tend to be by far the largest and 46% of them are larger than 60 Å3. The largest cavity observed in a protein–nucleic-acid interface is of type PDP and shown in Figure 3. The larger cavities are usually solvated (Figure 2b and c). Totally 75% and 66% of PD and PR cavities are solvated, respectively (considering the volume, the percentages are 88% and 85%, respectively). As was inferred from the data in Supplementary Table S3a, when grouped in different functional classes the PD cavities belonging to excision and/or repair enzymes contain more number of larger cavities (>100 Å3) followed by enzymes, ‘Others’ and transcription factors (Supplementary Figure S3).Figure 2.


Cavities in protein-DNA and protein-RNA interfaces.

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

The largest PDP cavity located in 1mdy (volume 828 Å3, Rvs 0.59 and 9 water molecules).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: The largest PDP cavity located in 1mdy (volume 828 Å3, Rvs 0.59 and 9 water molecules).
Mentions: The total volume of the cavities in individual interface is poorly correlated with the interface size (defined by number of atoms present in the interface) (Supplementary Figure S1), as was observed in protein–protein interfaces. However, for individual cavities one can use power law or linear fit (Supplementary Table S4) to express the variation of the volume with the number of atoms or residues lining the cavity (Supplementary Figure S2). Typical of tertiary structure cavities (10), approximately five atoms or four cavity-lining residues are needed to accommodate one water molecule. The distribution of volumes of cavities is shown in Figure 2a. Like the cavities in protein–protein interfaces, protein–nucleic-acid interfaces also contain higher percentage of cavities that are larger than 100 Å3—7.2 and 6.5% for PD and PR cavities, relative to 2.6% in cavities in the tertiary structure. However, the PDP cavities tend to be by far the largest and 46% of them are larger than 60 Å3. The largest cavity observed in a protein–nucleic-acid interface is of type PDP and shown in Figure 3. The larger cavities are usually solvated (Figure 2b and c). Totally 75% and 66% of PD and PR cavities are solvated, respectively (considering the volume, the percentages are 88% and 85%, respectively). As was inferred from the data in Supplementary Table S3a, when grouped in different functional classes the PD cavities belonging to excision and/or repair enzymes contain more number of larger cavities (>100 Å3) followed by enzymes, ‘Others’ and transcription factors (Supplementary Figure S3).Figure 2.

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