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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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2
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Tsuji T, Nagata T, Yanagawa H. N- and C-terminal Fragments of a Globular Protein Constructed by Elongation of Modules as a Units Associated for Functional Complementation. J Biochem 2008; 144:513-21. [DOI: 10.1093/jb/mvn099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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3
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Shinoda K, Takahashi KI, Go M. Retention of local conformational compactness in unfolding of barnase; Contribution of end-to-end interactions within quasi-modules. Biophysics (Nagoya-shi) 2007; 3:1-12. [PMID: 27857562 PMCID: PMC5036653 DOI: 10.2142/biophysics.3.1] [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: 03/05/2007] [Accepted: 04/11/2007] [Indexed: 12/01/2022] Open
Abstract
To understand how protein reduces the conformational space to be searched for the native structure, it is crucial to characterize ensembles of conformations on the way of folding processes, in particular ensembles of relatively long-range structures connecting between an extensively unfolded state and a state with a native-like overall chain topology. To analyze such intermediate conformations, we performed multiple unfolding molecular dynamics simulations of barnase at 498K. Some short-range structures such as part of helix and turn were well sustained while most of the secondary structures and the hydrophobic cores were eventually lost, which is consistent with the results by other experimental and computational studies. The most important novel findings were persistence of long-range relatively compact substructures, which was captured by exploiting the concept of module. Module is originally introduced to describe the hierarchical structure of a globular protein in the native state. Modules are conceptually such relatively compact substructures that are resulted from partitioning the native structure of a globular protein completely into several contiguous segments with the least extended conformations. We applied this concept of module to detect a possible hierarchical structure of each snapshot structure in unfolding processes as well. Along with this conceptual extension, such detected relatively compact substructures are named quasi-modules. We found almost perfect persistence of quasi-module boundaries that are positioned close to the native module boundaries throughout the unfolding trajectories. Relatively compact conformations of the quasi-modules seemed to be retained mainly by hydrophobic interactions formed between residues located at both terminal regions within each module. From these results, we propose a hypothesis that hierarchical folding with the early formation of quasi-modules effectively reduces search space for the native structure.
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Affiliation(s)
- Kazuki Shinoda
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Ken-Ichi Takahashi
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Mitiko Go
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan; Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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4
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Abstract
We have designed a minibarnase by removing one module from barnase, a bacterial RNase from Bacillus amyloliquefaciens. Barnase, consisting of 110 amino acid residues, is decomposed into six modules, M1-M6. Module is defined as a peptide segment consisting of contiguous amino acid residues that makes a small compact conformation within a globular domain. To understand the role of module in protein architecture, we analyzed NMR and CD spectra of a minibarnase, which lacked 26 amino acid residues corresponding to module M2. We demonstrated the formation of hydrophobic cores in the minibarnase similar to those of barnase. Although its conformational stability against acids and heat was reduced in comparison with barnase, the minibarnase retained cooperative folding character (two-state folding). Therefore, the folding of the minibarnase consisting of modules M1 and M3-M6 is independent to some extent of module M2. This finding may be useful for future module-based protein design.
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Affiliation(s)
- K Takahashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
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Affiliation(s)
- Z Y Peng
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06030, USA
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6
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Takahashi KI, Noguti T, Hojo H, Yamauchi K, Kinoshita M, Aimoto S, Ohkubo T, Gō M. A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation. PROTEIN ENGINEERING 1999; 12:673-80. [PMID: 10469828 DOI: 10.1093/protein/12.8.673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A globular domain can be decomposed into compact modules consisting of contiguous 10-30 amino acid residues. The correlation between modules and exons observed in different proteins suggests that each module was encoded by an ancestral exon and that modules were combined into globular domains by exon fusion. Barnase is a single domain RNase consisting of 110 amino acid residues and was decomposed into six modules. We designed a mini-protein by removing the second module, M2, from barnase in order to gain an insight into the structural and functional roles of the module. In the molecular modeling of the mini-protein, we evaluated thermodynamic stability and aqueous solubility together with mechanical stability of the model. We chemically synthesized a mini-barnase with (15)N-labeling at 10 residues, whose corresponding residues in barnase are all found in the region around the hydrophobic core. Circular dichroism and NMR measurements revealed that mini-barnase takes a non-random specific conformation that has a similar hydrophobic core structure to that of barnase. This result, that a module could be deleted without altering the structure of core region of barnase, supports the view that modules act as the building blocks of protein design.
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Affiliation(s)
- K i Takahashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
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7
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Tsuji T, Yoshida K, Satoh A, Kohno T, Kobayashi K, Yanagawa H. Foldability of barnase mutants obtained by permutation of modules or secondary structure units. J Mol Biol 1999; 286:1581-96. [PMID: 10064693 DOI: 10.1006/jmbi.1998.2558] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Modules, defined as stable, compact structure units in a globular protein, are good candidates for the construction of novel foldable proteins by permutation. Here we decomposed barnase into six modules (M1-M6) and constructed 23 barnase mutants containing permutations of the internal four (M2-M5) out of six modules. Globular proteins can also be subdivided into secondary structure units based on the extended structures that control the mutual relationships of the modules. We also decomposed barnase into six secondary structure units (S1-S6) and constructed 21 barnase mutants containing permutations of the internal four (S2-S5) out of six secondary structure units. Foldability of these two types of mutants was assessed by means of circular dichroism, fluorescence, and 1H-NMR measurements. A total of 15 of 23 module mutants and 15 of 21 secondary structure unit mutants formed definite secondary structures, such as alpha-helix and beta-sheet, at 20 microM owing to intermolecular interactions, but most of them converted to random coil structures at a lower concentration (1 microM). Of the 44 mutants, only two, M3245 and S2543, gave distinct near-UV CD spectra. S2543 especially showed definite signal dispersion in the amide and methyl regions of the 1H-NMR spectrum, though M3245 did not. Furthermore, urea-induced unfolding of S2543 monitored by far-UV CD and fluorescence measurements showed a distinct cooperative transition. These results strongly suggest that S2543 takes partially folded conformations in aqueous solution. Our results also suggest that building blocks such as secondary structure units capable of taking different stable conformations by adapting themselves to the surrounding environment, rather than building blocks such as modules having a specified stable conformation, are required for the formation of foldable proteins. Therefore, the use of secondary structure units for the construction of novel globular proteins is likely to be an effective approach.
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Affiliation(s)
- T Tsuji
- Department of Chemistry and Biotechnology, Yokohama National University, Tokiwadai Hodogaya-ku, Yokohama, 240, Japan
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8
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Shirai T, Fujikake M, Yamane T, Inaba K, Ishimori K, Morishima I. Design, construction, crystallization, and preliminary X-ray studies of a fine-tuning mutant (F133V) of module-substituted chimera hemoglobin. Proteins 1998; 32:263-7. [PMID: 9715902 DOI: 10.1002/(sici)1097-0134(19980815)32:3<263::aid-prot1>3.0.co;2-j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A chimera betaalpha-subunit of human hemoglobin was crystallized into a carbonmonoxy form. The protein was assembled by substituting the structural portion of a beta-subunit of hemoglobin (M4 module of the subunit) for its counterpart in the alpha-subunit. In order to overcome the inherent instability in the crystallization of the chimera subunit, a site-directed mutagenesis (F133V) technique was employed based on a computer model. The crystal was used for an X-ray diffraction study yielding a data set with a resolution of 2.5 A. The crystal belongs to the monoclinic space group P21, with cell dimensions of a = 62.9, b = 81.3, c = 55.1 A, and beta = 91.0 degrees . These dimensions are similar to the crystallographic parameters of the native beta-subunit tetramers in three different ligand states, one of which is a cyanide form that was also crystallized in this study.
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Affiliation(s)
- T Shirai
- Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering, Nagoya University, Japan.
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9
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Panchenko AR, Luthey-Schulten Z, Cole R, Wolynes PG. The foldon universe: a survey of structural similarity and self-recognition of independently folding units. J Mol Biol 1997; 272:95-105. [PMID: 9299340 DOI: 10.1006/jmbi.1997.1205] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have identified independently folding units, so called "foldons", from non-homologous proteins representing different folds. We applied simple statistical arguments in order to estimate the size of the foldon universe required to construct all foldable proteins. Various alignment procedures yield about 2600 foldons in the natural protein universe but this estimate is shown to be rather sensitive to the chosen cut-off value for structural similarity. We showed that foldon matching-modelling can reproduce the major part of the main chain of several proteins with a structural similarity measure Q-score of about 0.4 and an r.m.s. error of about 5 A, although the accuracy of structure prediction has been limited so far by the small size of foldon data set. The prediction score may be increased if one uses the set of protein fragments with optimized sequence-structure relationships, in other works, minimally frustrated segments. To quantify the degree of frustration of the structures of foldons from our database, we searched for those foldons which recognize their own sequence and structure upon threading. As a result we found that about half of the foldons from our data set recognize themselves as the best choice upon threading and therefore are individually minimally frustrated. We showed that there is a close connection between the Q-score of self recognition and the relative foldability (Theta) of the folding units. Foldons having high Q-score and Theta values are expected to be formed in the early phase of the folding process and be observed as stable intermediates under appropriate experimental conditions.
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Affiliation(s)
- A R Panchenko
- School of Chemical Sciences, University of Illinois, Urbana, IL 61801, USA
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10
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Abstract
NMR has emerged as an important tool for studies of protein folding because of the unique structural insights it can provide into many aspects of the folding process. Applications include measurements of kinetic folding events and structural characterization of folding intermediates, partly folded states, and unfolded states. Kinetic information on a time scale of milliseconds or longer can be obtained by real-time NMR experiments and by quench-flow hydrogen-exchange pulse labeling. Although NMR cannot provide direct information on the very rapid processes occurring during the earliest stages of protein folding, studies of isolated peptide fragments provide insights into likely protein folding initiation events. Multidimensional NMR techniques are providing new information on the structure and dynamics of protein folding intermediates and both partly folded and unfolded states.
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Affiliation(s)
- H J Dyson
- Scripps Research Institute, La Jolla, California 92037, USA
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11
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Panchenko AR, Luthey-Schulten Z, Wolynes PG. Foldons, protein structural modules, and exons. Proc Natl Acad Sci U S A 1996; 93:2008-13. [PMID: 8700876 PMCID: PMC39900 DOI: 10.1073/pnas.93.5.2008] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Foldons, which are kinetically competent, quasi-independently folding units of a protein, may be defined using energy landscape analysis. Foldons can be identified by maxima in a scan of the ratio of a contiguous segment's energetic stability gap to the energy variance of that segment's molten globule states, reflecting the requirement of minimal frustration. The predicted foldons are compared with the exons and structural modules for 16 of the 30 proteins studied. Statistical analysis indicates a strong correlation between the energetically determined foldons and Go's geometrically defined structural modules, but there are marked sequence-dependent effects. There is only a weak correlation of foldons to exons. For gammaII-crystallin, myoglobin, barnase, alpha-lactalbumin, and cytochrome c the foldons and some noncontiguous clusters of foldons compare well with intermediates observed in experiment.
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Affiliation(s)
- A R Panchenko
- School of Chemical Sciences, University of Illinois, Urbana 61801, USA
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12
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Abstract
Proteins in eukaryotes are composed of structural units, each encoded by discrete exons. The protein module is one such structural unit; it has been defined as the least extended or the most compact contiguous segment in a globular domain. To elucidate roles of modules in protein evolution and folding, we examined roles of hydrogen bonds and hydrophobic cores, as related to the stability of these modules. For this purpose we studied barnase, a bacterial RNase from Bacillus amylolique-faciens. Barnase is decomposed into at least six modules, M1-M6; the module boundaries are identified at amino acid residues 24, 52, 73, 88, and 98. Hydrogen bonds are localized mainly within each of the modules, with only a few between them, thereby indicating that their locations are designed to primarily stabilize each individual module. To obtain support for this notion, an analysis was made of hypothetical modules defined as segments starting at a center of one module and ending at the center of the following one. We found that the hydrogen bonds did not localize in each hypothetical module and that many formed between the hypothetical modules. The native conformations of modules of barnase may be specified predominantly by interactions within the modules.
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Affiliation(s)
- T Noguti
- Department of Biology, Faculty of Science, Nagoya University, Japan
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