Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins.
Here we present a systematic analysis of accessible surface areas and hydrogen bonds of 2554 globular proteins from four structural classes (all-α, all-β, α/β and α+β proteins) that is aimed to learn in which structural class the accessible surface area increases with increasing protein molecular ma...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2011-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3228773?pdf=render |
| _version_ | 1818545160241283072 |
|---|---|
| author | Anna V Glyakina Natalya S Bogatyreva Oxana V Galzitskaya |
| author_facet | Anna V Glyakina Natalya S Bogatyreva Oxana V Galzitskaya |
| author_sort | Anna V Glyakina |
| collection | DOAJ |
| description | Here we present a systematic analysis of accessible surface areas and hydrogen bonds of 2554 globular proteins from four structural classes (all-α, all-β, α/β and α+β proteins) that is aimed to learn in which structural class the accessible surface area increases with increasing protein molecular mass more rapidly than in other classes, and what structural peculiarities are responsible for this effect. The beta structural class of proteins was found to be the leader, with the following possible explanations of this fact. First, in beta structural proteins, the fraction of residues not included in the regular secondary structure is the largest, and second, the accessible surface area of packaged elements of the beta-structure increases more rapidly with increasing molecular mass in comparison with the alpha-structure. Moreover, in the beta structure, the probability of formation of backbone hydrogen bonds is higher than that in the alpha helix for all residues of α+β proteins (the average probability is 0.73±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without proline) and α/β proteins, except for asparagine, aspartic acid, glycine, threonine, and serine (0.70±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without the proline residue). There is a linear relationship between the number of hydrogen bonds and the number of amino acid residues in the protein (Number of hydrogen bonds=0.678·number of residues-3.350). |
| first_indexed | 2024-12-11T22:57:53Z |
| format | Article |
| id | doaj.art-6371ba6002be4ba9988a2bd6efe4d00a |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T22:57:53Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-6371ba6002be4ba9988a2bd6efe4d00a2022-12-22T00:47:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-01612e2846410.1371/journal.pone.0028464Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins.Anna V GlyakinaNatalya S BogatyrevaOxana V GalzitskayaHere we present a systematic analysis of accessible surface areas and hydrogen bonds of 2554 globular proteins from four structural classes (all-α, all-β, α/β and α+β proteins) that is aimed to learn in which structural class the accessible surface area increases with increasing protein molecular mass more rapidly than in other classes, and what structural peculiarities are responsible for this effect. The beta structural class of proteins was found to be the leader, with the following possible explanations of this fact. First, in beta structural proteins, the fraction of residues not included in the regular secondary structure is the largest, and second, the accessible surface area of packaged elements of the beta-structure increases more rapidly with increasing molecular mass in comparison with the alpha-structure. Moreover, in the beta structure, the probability of formation of backbone hydrogen bonds is higher than that in the alpha helix for all residues of α+β proteins (the average probability is 0.73±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without proline) and α/β proteins, except for asparagine, aspartic acid, glycine, threonine, and serine (0.70±0.01 for the beta-structure and 0.60±0.01 for the alpha-structure without the proline residue). There is a linear relationship between the number of hydrogen bonds and the number of amino acid residues in the protein (Number of hydrogen bonds=0.678·number of residues-3.350).http://europepmc.org/articles/PMC3228773?pdf=render |
| spellingShingle | Anna V Glyakina Natalya S Bogatyreva Oxana V Galzitskaya Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. PLoS ONE |
| title | Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. |
| title_full | Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. |
| title_fullStr | Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. |
| title_full_unstemmed | Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. |
| title_short | Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. |
| title_sort | accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins |
| url | http://europepmc.org/articles/PMC3228773?pdf=render |
| work_keys_str_mv | AT annavglyakina accessiblesurfacesofbetaproteinsincreasewithincreasingproteinmolecularmassmorerapidlythanthoseofotherproteins AT natalyasbogatyreva accessiblesurfacesofbetaproteinsincreasewithincreasingproteinmolecularmassmorerapidlythanthoseofotherproteins AT oxanavgalzitskaya accessiblesurfacesofbetaproteinsincreasewithincreasingproteinmolecularmassmorerapidlythanthoseofotherproteins |