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Bagrova O, Lapshina K, Sidorova A, Shpigun D, Lutsenko A, Belova E. Secondary structure analysis of proteins within the same topology group. Biochem Biophys Res Commun 2024; 734:150613. [PMID: 39222577 DOI: 10.1016/j.bbrc.2024.150613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/13/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
The native conformation of a protein plays a decisive role in ensuring its functionality. It is established that the spatial structure of proteins may exhibit a greater degree of conservation than the corresponding amino acid sequences. This study aims to clarify structural distinctions between homologous and non-homologous proteins with identical topology. The analysis focuses on secondary structures with special emphasis on their fraction, distribution along the polypeptide chain, and chirality. Three different groups of proteins with identical topology were considered according to the CATH database: a homologous group of Globins, a group of Phycocyanins, which is often considered as a potential relative of globins, and a diverse assembly of other globin-like proteins. Some structural patterns in the distribution of secondary structure have been identified within Globins. A similar profile was observed in Phycocyanins, in contrast to the third group. In addition, a distinguishable structural motif, including structures such as 310-helix and irregular structure, has been found in both Globins and Phycocyanins, which can be proposed as an evolutionary imprint.
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Affiliation(s)
- Olga Bagrova
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Ksenia Lapshina
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alla Sidorova
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Denis Shpigun
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Aleksey Lutsenko
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ekaterina Belova
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
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Jones AA, Snow CD. Porous protein crystals: synthesis and applications. Chem Commun (Camb) 2024; 60:5790-5803. [PMID: 38756076 DOI: 10.1039/d4cc00183d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Large-pore protein crystals (LPCs) are an emerging class of biomaterials. The inherent diversity of proteins translates to a diversity of crystal lattice structures, many of which display large pores and solvent channels. These pores can, in turn, be functionalized via directed evolution and rational redesign based on the known crystal structures. LPCs possess extremely high solvent content, as well as extremely high surface area to volume ratios. Because of these characteristics, LPCs continue to be explored in diverse applications including catalysis, targeted therapeutic delivery, templating of nanostructures, structural biology. This Feature review article will describe several of the existing platforms in detail, with particular focus on LPC synthesis approaches and reported applications.
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Affiliation(s)
- Alec Arthur Jones
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
| | - Christopher D Snow
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA
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Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths. Proc Natl Acad Sci U S A 2017; 114:11703-11708. [PMID: 29078314 PMCID: PMC5676897 DOI: 10.1073/pnas.1707642114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We question a central paradigm: namely, that the protein domain is the “atomic unit” of evolution. In conflict with the current textbook view, our results unequivocally show that duplication of protein segments happens both above and below the domain level among amino acid segments of diverse lengths. Indeed, we show that significant evolutionary information is lost when the protein is approached as a string of domains. Our finer-grained approach reveals a far more complicated picture, where reused segments often intertwine and overlap with each other. Our results are consistent with a recursive model of evolution, in which segments of various lengths, typically smaller than domains, “hop” between environments. The fit segments remain, leaving traces that can still be detected. Proteins share similar segments with one another. Such “reused parts”—which have been successfully incorporated into other proteins—are likely to offer an evolutionary advantage over de novo evolved segments, as most of the latter will not even have the capacity to fold. To systematically explore the evolutionary traces of segment “reuse” across proteins, we developed an automated methodology that identifies reused segments from protein alignments. We search for “themes”—segments of at least 35 residues of similar sequence and structure—reused within representative sets of 15,016 domains [Evolutionary Classification of Protein Domains (ECOD) database] or 20,398 chains [Protein Data Bank (PDB)]. We observe that theme reuse is highly prevalent and that reuse is more extensive when the length threshold for identifying a theme is lower. Structural domains, the best characterized form of reuse in proteins, are just one of many complex and intertwined evolutionary traces. Others include long themes shared among a few proteins, which encompass and overlap with shorter themes that recur in numerous proteins. The observed complexity is consistent with evolution by duplication and divergence, and some of the themes might include descendants of ancestral segments. The observed recursive footprints, where the same amino acid can simultaneously participate in several intertwined themes, could be a useful concept for protein design. Data are available at http://trachel-srv.cs.haifa.ac.il/rachel/ppi/themes/.
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Paeth M, Stapleton J, Dougherty ML, Fischesser H, Shepherd J, McCauley M, Falatach R, Page RC, Berberich JA, Konkolewicz D. Approaches for Conjugating Tailor-Made Polymers to Proteins. Methods Enzymol 2017; 590:193-224. [DOI: 10.1016/bs.mie.2016.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Williams C, Dougherty ML, Makaroff K, Stapleton J, Konkolewicz D, Berberich JA, Page RC. Strategies for Biophysical Characterization of Protein–Polymer Conjugates. Methods Enzymol 2017; 590:93-114. [DOI: 10.1016/bs.mie.2016.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Motomura K, Fujita T, Tsutsumi M, Kikuzato S, Nakamura M, Otaki JM. Word decoding of protein amino Acid sequences with availability analysis: a linguistic approach. PLoS One 2012; 7:e50039. [PMID: 23185527 PMCID: PMC3503725 DOI: 10.1371/journal.pone.0050039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/15/2012] [Indexed: 11/19/2022] Open
Abstract
The amino acid sequences of proteins determine their three-dimensional structures and functions. However, how sequence information is related to structures and functions is still enigmatic. In this study, we show that at least a part of the sequence information can be extracted by treating amino acid sequences of proteins as a collection of English words, based on a working hypothesis that amino acid sequences of proteins are composed of short constituent amino acid sequences (SCSs) or "words". We first confirmed that the English language highly likely follows Zipf's law, a special case of power law. We found that the rank-frequency plot of SCSs in proteins exhibits a similar distribution when low-rank tails are excluded. In comparison with natural English and "compressed" English without spaces between words, amino acid sequences of proteins show larger linear ranges and smaller exponents with heavier low-rank tails, demonstrating that the SCS distribution in proteins is largely scale-free. A distribution pattern of SCSs in proteins is similar among species, but species-specific features are also present. Based on the availability scores of SCSs, we found that sequence motifs are enriched in high-availability sites (i.e., "key words") and vice versa. In fact, the highest availability peak within a given protein sequence often directly corresponds to a sequence motif. The amino acid composition of high-availability sites within motifs is different from that of entire motifs and all protein sequences, suggesting the possible functional importance of specific SCSs and their compositional amino acids within motifs. We anticipate that our availability-based word decoding approach is complementary to sequence alignment approaches in predicting functionally important sites of unknown proteins from their amino acid sequences.
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Affiliation(s)
- Kenta Motomura
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Department of Information Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tomohiro Fujita
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Motosuke Tsutsumi
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Satsuki Kikuzato
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Morikazu Nakamura
- Department of Information Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Joji M. Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, Japan
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Petersen SB, Neves-Petersen MT, Henriksen SB, Mortensen RJ, Geertz-Hansen HM. Scale-free behaviour of amino acid pair interactions in folded proteins. PLoS One 2012; 7:e41322. [PMID: 22848462 PMCID: PMC3406053 DOI: 10.1371/journal.pone.0041322] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 06/20/2012] [Indexed: 11/19/2022] Open
Abstract
The protein structure is a cumulative result of interactions between amino acid residues interacting with each other through space and/or chemical bonds. Despite the large number of high resolution protein structures, the "protein structure code" has not been fully identified. Our manuscript presents a novel approach to protein structure analysis in order to identify rules for spatial packing of amino acid pairs in proteins. We have investigated 8706 high resolution non-redundant protein chains and quantified amino acid pair interactions in terms of solvent accessibility, spatial and sequence distance, secondary structure, and sequence length. The number of pairs found in a particular environment is stored in a cell in an 8 dimensional data tensor. When plotting the cell population against the number of cells that have the same population size, a scale free organization is found. When analyzing which amino acid paired residues contributed to the cells with a population above 50, pairs of Ala, Ile, Leu and Val dominate the results. This result is statistically highly significant. We postulate that such pairs form "structural stability points" in the protein structure. Our data shows that they are in buried α-helices or β-strands, in a spatial distance of 3.8-4.3Å and in a sequence distance >4 residues. We speculate that the scale free organization of the amino acid pair interactions in the 8D protein structure combined with the clear dominance of pairs of Ala, Ile, Leu and Val is important for understanding the very nature of the protein structure formation. Our observations suggest that protein structures should be considered as having a higher dimensional organization.
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Affiliation(s)
- Steffen B. Petersen
- Int Iberian Nanotechnol Laboratory INL, Braga, Portugal
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- The Institute for Lasers, University at Buffalo, The State University of New York at Buffalo, Photonics and Biophotonics, Buffalo, New York, United States of America
| | - Maria Teresa Neves-Petersen
- Int Iberian Nanotechnol Laboratory INL, Braga, Portugal
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Svend B. Henriksen
- Department of Physics and Nanotechnology, Aalborg University, Aalborg, Denmark
| | - Rasmus J. Mortensen
- Department of Physics and Nanotechnology, Aalborg University, Aalborg, Denmark
- Department of Infectious Disease Immunology, Statens Serum Institute, Copenhagen, Denmark
| | - Henrik M. Geertz-Hansen
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability Fremtidsvej, Hørsholm, Copenhagen, Denmark
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Tomii K, Sawada Y, Honda S. Convergent evolution in structural elements of proteins investigated using cross profile analysis. BMC Bioinformatics 2012; 13:11. [PMID: 22244085 PMCID: PMC3398312 DOI: 10.1186/1471-2105-13-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 01/16/2012] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess local similarities in both sequence and structure across protein folds. However, to capture more precise sequence-structure relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary information. The former are generally regarded as representing the amino acid preferences at each position of a specific conformation of protein segment. They might reflect the nature of ancient short peptide ancestors, using the results of structural classifications of protein segments. Results This report describes the development and use of "Cross Profile Analysis" to compare sequence-based profiles and structure-based profiles based on amino acid occurrences at each position within a protein segment cluster. Using systematic cross profile analysis, we found structural clusters of 9-residue and 15-residue segments showing remarkably strong correlation with particular sequence profiles. These correlations reflect structural similarities among constituent segments of both sequence-based and structure-based profiles. We also report previously undetectable sequence-structure patterns that transcend protein family and fold boundaries, and present results of the conformational analysis of the deduced peptide of a segment cluster. These results suggest the existence of ancient short-peptide ancestors. Conclusions Cross profile analysis reveals the polyphyletic and convergent evolution of β-hairpin-like structures, which were verified both experimentally and computationally. The results presented here give us new insights into the evolution of short protein segments.
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Ito JI, Sonobe Y, Ikeda K, Tomii K, Higo J. Universal partitioning of the hierarchical fold network of 50-residue segments in proteins. BMC STRUCTURAL BIOLOGY 2009; 9:34. [PMID: 19454039 PMCID: PMC2693521 DOI: 10.1186/1472-6807-9-34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 05/20/2009] [Indexed: 11/23/2022]
Abstract
Background Several studies have demonstrated that protein fold space is structured hierarchically and that power-law statistics are satisfied in relation between the numbers of protein families and protein folds (or superfamilies). We examined the internal structure and statistics in the fold space of 50 amino-acid residue segments taken from various protein folds. We used inter-residue contact patterns to measure the tertiary structural similarity among segments. Using this similarity measure, the segments were classified into a number (Kc) of clusters. We examined various Kc values for the clustering. The special resolution to differentiate the segment tertiary structures increases with increasing Kc. Furthermore, we constructed networks by linking structurally similar clusters. Results The network was partitioned persistently into four regions for Kc ≥ 1000. This main partitioning is consistent with results of earlier studies, where similar partitioning was reported in classifying protein domain structures. Furthermore, the network was partitioned naturally into several dozens of sub-networks (i.e., communities). Therefore, intra-sub-network clusters were mutually connected with numerous links, although inter-sub-network ones were rarely done with few links. For Kc ≥ 1000, the major sub-networks were about 40; the contents of the major sub-networks were conserved. This sub-partitioning is a novel finding, suggesting that the network is structured hierarchically: Segments construct a cluster, clusters form a sub-network, and sub-networks constitute a region. Additionally, the network was characterized by non-power-law statistics, which is also a novel finding. Conclusion Main findings are: (1) The universe of 50 residue segments found here was characterized by non-power-law statistics. Therefore, the universe differs from those ever reported for the protein domains. (2) The 50-residue segments were partitioned persistently and universally into some dozens (ca. 40) of major sub-networks, irrespective of the number of clusters. (3) These major sub-networks encompassed 90% of all segments. Consequently, the protein tertiary structure is constructed using the dozens of elements (sub-networks).
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Nacher JC, Hayashida M, Akutsu T. Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs. Biosystems 2008; 95:155-9. [PMID: 19010382 DOI: 10.1016/j.biosystems.2008.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Revised: 10/03/2008] [Accepted: 10/05/2008] [Indexed: 11/18/2022]
Abstract
Recent analyses of biological and artificial networks have revealed a common network architecture, called scale-free topology. The origin of the scale-free topology has been explained by using growth and preferential attachment mechanisms. In a cell, proteins are the most important carriers of function, and are composed of domains as elemental units responsible for the physical interaction between protein pairs. Here, we propose a model for protein-protein interaction networks that reveals the emergence of two possible topologies. We show that depending on the number of randomly selected interacting domain pairs, the connectivity distribution follows either a scale-free distribution, even in the absence of the preferential attachment, or a normal distribution. This new approach only requires an evolutionary model of proteins (nodes) but not for the interactions (edges). The edges are added by means of random interaction of domain pairs. As a result, this model offers a new mechanistic explanation for understanding complex networks with a direct biological interpretation because only protein structures and their functions evolved through genetic modifications of amino acid sequences. These findings are supported by numerical simulations as well as experimental data.
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Affiliation(s)
- J C Nacher
- Department of Complex Systems, Future University-Hakodate, 116-2 Kamedanakano-cho Hakodate, Hokkaido 041-8655, Japan.
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Honda S, Akiba T, Kato YS, Sawada Y, Sekijima M, Ishimura M, Ooishi A, Watanabe H, Odahara T, Harata K. Crystal structure of a ten-amino acid protein. J Am Chem Soc 2008; 130:15327-31. [PMID: 18950166 DOI: 10.1021/ja8030533] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
What is the smallest protein? This is actually not such a simple question to answer, because there is no established consensus among scientists as to the definition of a protein. We describe here a designed molecule consisting of only 10 amino acids. Despite its small size, its essential characteristics, revealed by its crystal structure, solution structure, thermal stability, free energy surface, and folding pathway network, are consistent with the properties of natural proteins. The existence of this kind of molecule deepens our understanding of proteins and impels us to define an "ideal protein" without inquiring whether the molecule actually occurs in nature.
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Affiliation(s)
- Shinya Honda
- National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba 305-8566, Japan.
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Sawada Y, Honda S. ProSeg: a database of local structures of protein segments. J Comput Aided Mol Des 2008; 23:163-9. [DOI: 10.1007/s10822-008-9248-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 09/26/2008] [Indexed: 11/29/2022]
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Ikeda K, Hirokawa T, Higo J, Tomii K. Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces. BMC STRUCTURAL BIOLOGY 2008; 8:37. [PMID: 18700043 PMCID: PMC2529298 DOI: 10.1186/1472-6807-8-37] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 08/13/2008] [Indexed: 12/05/2022]
Abstract
Background Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the conformational space of segments with intermediate length between short segments and domains remain unclear. Conformational spaces of intermediate length segments probably differ from those of short segments. We investigated the identification and characterization of the boundary(s) between peptide-like (short segment) and protein-like (long segment) distributions. We generated ensembles embedded in globular proteins comprising segments 10–50 residues long. We explored the relationships between the conformational distribution of segments and their lengths, and also protein structural classes using principal component analysis based on the intra-segment Cα-Cα atomic distances. Results Our statistical analyses of segment conformations and length revealed critical dual transitions in their conformational distribution with segments derived from all four structural classes. Dual transitions were identified with the intermediate phase between the short segments and domains. Consequently, protein segment universes were categorized. i) Short segments (10–22 residues) showed a distribution with a high frequency of secondary structure clusters. ii) Medium segments (23–26 residues) showed a distribution corresponding to an intermediate state of transitions. iii) Long segments (27–50 residues) showed a distribution converging on one huge cluster containing compact conformations with a smaller radius of gyration. This distribution reflects the protein structures' organization and protein domains' origin. Three major conformational components (radius of gyration, structural symmetry with respect to the N-terminal and C-terminal halves, and single-turn/two-turn structure) well define most of the segment universes. Furthermore, we identified several conformational components that were unique to each structural class. Those characteristics suggest that protein segment conformation is described by compositions of the three common structural variables with large contributions and specific structural variables with small contributions. Conclusion The present results of the analyses of four protein structural classes show the universal role of three major components as segment conformational descriptors. The obtained perspectives of distribution changes related to the segment lengths using the three key components suggest both the adequacy and the possibility of further progress on the prediction strategies used in the recent de novo structure-prediction methods.
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Affiliation(s)
- Kazuyoshi Ikeda
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.
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Manikandan K, Pal D, Ramakumar S, Brener NE, Iyengar SS, Seetharaman G. Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. Genome Biol 2008; 9:R52. [PMID: 18331637 PMCID: PMC2397504 DOI: 10.1186/gb-2008-9-3-r52] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 02/24/2008] [Accepted: 03/10/2008] [Indexed: 11/25/2022] Open
Abstract
A geometric clustering algorithm has been developed to dissect protein fragments based on their relevance to function. We have developed a geometric clustering algorithm using backbone φ,ψ angles to group conformationally similar peptide fragments of any length. By labeling each fragment in the cluster with the level-specific Gene Ontology 'molecular function' term of its protein, we are able to compute statistics for molecular function-propensity and p-value of individual fragments in the cluster. Clustering-cum-statistical analysis for peptide fragments 8 residues in length and with only trans peptide bonds shows that molecular function propensities ≥20 and p-values ≤0.05 can dissect fragments within a protein linked to the molecular function.
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