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Kanduc D. Homology, similarity, and identity in peptide epitope immunodefinition. J Pept Sci 2012; 18:487-94. [PMID: 22696298 DOI: 10.1002/psc.2419] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 04/10/2012] [Accepted: 04/25/2012] [Indexed: 01/03/2023]
Abstract
The tendency to use the terms homology, similarity, and identity interchangeably persists in comparative biology. When translated to immunology, overlapping the concepts of homology, similarity, and identity complicates the exact definition of the self-nonself dichotomy and, in particular, affects immunopeptidomics, an emerging field aimed at cataloging and distinguishing immunoreactive peptide epitopes from silent nonreactive amino acid sequences. The definition of similar/dissimilar peptides in immunology is discussed with special attention to the analysis of immunological (dis)similarity between two or more protein sequences that equates to measuring sequence similarity with the use of a proper measurement unit such as a length determinant.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy.
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Shiba R, Umeyama M, Tsukasa S, Kamikubo H, Yamazaki Y, Yamaguchi M, Iwakura M, Kataoka M. Systematic alanine insertion reveals the essential regions that encode structure formation and activity of dihydrofolate reductase. Biophysics (Nagoya-shi) 2011; 7:1-10. [PMID: 27857587 PMCID: PMC5036773 DOI: 10.2142/biophysics.7.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 12/07/2010] [Indexed: 12/01/2022] Open
Abstract
Decoding sequence information is equivalent to elucidating the design principles of proteins. For this purpose, we conducted systematic alanine insertion analysis to reveal the regions in the primary structure where the sequence continuity cannot be disrupted. We applied this method to dihydrofolate reductase (DHFR), and examined the effects of alanine insertion on structure and the enzymatic activity by solubility assay and trimethoprim resistance, respectively. We revealed that DHFR is composed of “Structure Elements”, “Function Elements” and linkers connecting these elements. The “Elements” are defined as regions where the alanine insertion caused DHFR to become unstructured or inactive. Some “Structure Elements” overlap with “Function Elements”, indicating that loss of structure leads to loss of function. However, other “Structure Elements” are not “Function Elements”, in that alanine insertion mutants of these regions exhibit substrate- or inhibitor-induced folding. There are also some “Function Elements” which are not “Structure Elements”; alanine insertion into these elements deforms the catalytic site topology without the loss of tertiary structure. We hypothesize that these elements are involved essential interactions for structure formation and functional expression. The “Elements” are closely related to the module structure of DHFR. An “Element” belongs to a single module, and a single module is composed of some number of “Elements.” We propose that properties of a module are determined by the “Elements” it contains. Systematic alanine insertion analysis is an effective and unique method for deriving the regions of a sequence that are essential for structure formation and functional expression.
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Affiliation(s)
- Rumi Shiba
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Mika Umeyama
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Sayaka Tsukasa
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Yoichi Yamazaki
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Mariko Yamaguchi
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Masahiro Iwakura
- Protein Design Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
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Loughman JA, Caparon MG. Contribution of invariant residues to the function of Rgg family transcription regulators. J Bacteriol 2006; 189:650-5. [PMID: 17098902 PMCID: PMC1797381 DOI: 10.1128/jb.01437-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Rgg family of transcription regulators is widely distributed among gram-positive bacteria, yet how these proteins control transcription is poorly understood. Using Streptococcus pyogenes RopB as a model, we demonstrated that residues invariant among Rgg-like regulators are critical for function and obtained evidence for a mechanism involving protein complex formation.
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Affiliation(s)
- Jennifer A Loughman
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110-1093, USA
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Kitamura K, Yoshida C, Nishigaki K. GFPs of insertion mutation generated by molecular size-altering block shuffling. FEBS Lett 2004; 555:483-8. [PMID: 14675760 DOI: 10.1016/s0014-5793(03)01308-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Insertion and deletion analyses of a protein have been less common than point mutation analyses, partly due to the lack in effective methods. This is the case with the green fluorescent protein (GFP), which is so widely applied in molecular biology and other fields. In this paper we first introduce a systematic approach for generating insertion/deletion mutants of GFP. A new technology of Y-ligation-based block shuffling (YLBS) was successfully applied to produce size-altered GFPs, providing insertion-containing GFPs of fluorescence, though no deletion type of fluorescence was obtained so far as examined. The analysis of these proteins suggested that size alteration (deletion/insertion) is acceptable so far as some type of rearrangement in a local structure can accommodate it. This paper demonstrates that YLBS can generate insertion and deletion mutant libraries systematically, which are beneficial in the study of structure-function relationship.
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Affiliation(s)
- Koichiro Kitamura
- Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
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Wada T, Yamazaki T, Kyogoku Y. The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus. J Biol Chem 2000; 275:16057-63. [PMID: 10821859 DOI: 10.1074/jbc.275.21.16057] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The C-terminal domain of the alpha subunit of the RNA polymerase (alphaCTD) from Escherichia coli (Ec) regulates transcription by interacting with many kinds of proteins and promoter upstream (UP) elements consisting of AT-rich sequences. However, it is unclear how this system is common in all eubacteria. We investigate the structure and properties of alphaCTD from an extremely thermophilic eubacterium, Thermus thermophilus (Tt). The solution structure of Tt alphaCTD (85 amino acids) was determined by NMR, and the interaction between Tt alphaCTD and DNA with different sequences was investigated by means of chemical shift perturbation experiments. The tertiary structure of Tt alphaCTD is almost identical with that of Ec alphaCTD despite 32% sequence homology. However, Tt alphaCTD interacts with the upstream region sequence of the promoter in the Tt 16 S ribosomal protein operon rather than the Ec UP element DNA. The upstream region sequence of Tt is composed of 25 base pairs with 40% AT, unlike the Ec UP element with 80% AT. The DNA binding site in Tt alphaCTD is located on the surface composed of helix 4 and the loop preceding helix 4. The electric charges on this surface are not remarkably localized like those of Ec alphaCTD.
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Affiliation(s)
- T Wada
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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