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Kimura R, Aumpuchin P, Hamaue S, Shimomura T, Kikuchi T. Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Gō-model simulations. BMC Mol Cell Biol 2020; 21:28. [PMID: 32295515 PMCID: PMC7477875 DOI: 10.1186/s12860-020-00271-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
Background The details of the folding mechanisms have not yet been fully understood for many proteins, and it is believed that the information on the folding mechanism of a protein is encoded in its amino acid sequence. β-trefoil proteins are known to have the same 3D scaffold, namely, a three-fold symmetric scaffold, despite the proteins’ low sequence identity among superfamilies. In this study, we extract an initial folding unit from the amino acid sequences of irregular β-trefoil proteins by constructing an average distance map (ADM) and utilizing inter-residue average distance statistics to determine the relative contact frequencies for residue pairs in terms of F values. We compare our sequence-based prediction results with the packing between hydrophobic residues in native 3D structures and a Gō-model simulation. Results The ADM and F-value analyses predict that the N-terminal and C-terminal regions are compact and that the hydrophobic residues at the central region can be regarded as an interaction center with other residues. These results correspond well to those of the Gō-model simulations. Moreover, our results indicate that the irregular parts in the β-trefoil proteins do not hinder the protein formation. Conserved hydrophobic residues on the β5 strand are always the interaction center of packing between the conserved hydrophobic residues in both regular and irregular β-trefoil proteins. Conclusions We revealed that the β5 strand plays an important role in β-trefoil protein structure construction. The sequence-based methods used in this study can extract the protein folding information from only amino acid sequence data, and well corresponded to 3D structure-based Gō-model simulation and available experimental results.
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Affiliation(s)
- Risako Kimura
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Panyavut Aumpuchin
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Shoya Hamaue
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takumi Shimomura
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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2
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Aumpuchin P, Hamaue S, Kikuchi T. Prediction of the initial folding sites and the entire folding processes for Ig-like beta-sandwich proteins. Proteins 2019; 88:740-758. [PMID: 31833097 DOI: 10.1002/prot.25862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 11/13/2019] [Accepted: 12/06/2019] [Indexed: 11/12/2022]
Abstract
Describing the whole story of protein folding is currently the main enigmatic problem in molecular bioinformatics study. Protein folding mechanisms have been intensively investigated with experimental as well as simulation techniques. Since a protein folds into its specific 3D structure from a unique amino acid sequence, it is interesting to extract as much information as possible from the amino acid sequence of a protein. Analyses based on inter-residue average distance statistics and a coarse-grained Gō-model simulation were conducted on Ig and FN3 domains of a titin protein to decode the folding mechanisms from their sequence data and native structure data, respectively. The central region of all domains was predicted to be an initial folding unit, that is, stable in an early state of folding. This common feature coincides well with the experimental results and underscores the significance of the β-sandwich proteins' common structure, namely, the key strands for folding and the Greek-key motif, which is located in the central region. We confirmed that our sequence-based techniques were able to predict the initial folding event just next to the denatured state and that a 3D-based Gō-model simulation can be used to investigate the whole process of protein folding.
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Affiliation(s)
- Panyavut Aumpuchin
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Shoya Hamaue
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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3
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Shimomura T, Nishijima K, Kikuchi T. A new technique for predicting intrinsically disordered regions based on average distance map constructed with inter-residue average distance statistics. BMC STRUCTURAL BIOLOGY 2019; 19:3. [PMID: 30727987 PMCID: PMC6366092 DOI: 10.1186/s12900-019-0101-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 01/23/2019] [Indexed: 01/03/2023]
Abstract
Background It had long been thought that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions. However, subsequent research has shown that there are many proteins without specific 3D-structures under physiological conditions, so-called intrinsically disordered proteins (IDPs). This study presents a new technique for predicting intrinsically disordered regions in a protein, based on our average distance map (ADM) technique. The ADM technique was developed to predict compact regions or structural domains in a protein. In a protein containing partially disordered regions, a domain region is likely to be ordered, thus it is unlikely that a disordered region would be part of any domain. Therefore, the ADM technique is expected to also predict a disordered region between domains. Results The results of our new technique are comparable to the top three performing techniques in the community-wide CASP10 experiment. We further discuss the case of p53, a tumor-suppressor protein, which is the most significant protein among cell cycle regulatory proteins. This protein exhibits a disordered character as a monomer but an ordered character when two p53s form a dimer. Conclusion Our technique can predict the location of an intrinsically disordered region in a protein with an accuracy comparable to the best techniques proposed so far. Furthermore, it can also predict a core region of IDPs forming definite 3D structures through interactions, such as dimerization. The technique in our study may also serve as a means of predicting a disordered region which would become an ordered structure when binding to another protein. Electronic supplementary material The online version of this article (10.1186/s12900-019-0101-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takumi Shimomura
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Kohki Nishijima
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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4
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Aumpuchin P, Kikuchi T. Prediction of folding mechanisms for Ig-like beta sandwich proteins based on inter-residue average distance statistics methods. Proteins 2018; 87:120-135. [PMID: 30520530 DOI: 10.1002/prot.25637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/05/2018] [Accepted: 11/29/2018] [Indexed: 11/11/2022]
Abstract
To understand the folding mechanism of a protein is one of the goals in bioinformatics study. Nowadays, it is enigmatic and difficult to extract folding information from amino acid sequence using standard bioinformatics techniques or even experimental protocols which can be time consuming. To overcome these problems, we aim to extract the initial folding unit for titin protein (Ig and fnIII domains) by means of inter-residue average distance statistics, Average Distance Map (ADM) and contact frequency analysis (F-value). TI I27 and TNfn3 domains are used to represent the Ig-domain and fnIII-domain, respectively. Beta-strands 2, 3, 5, and 6 are significant for the initial folding processes of TI I27. The central strands of TNfn3 were predicted as a primary folding segment. Known 3D structure and unknown 3D structure domains were investigated by structure or non-structure based multiple sequence alignment, respectively, to learn the conserved hydrophobic residues and predicted compact region relevant to evolution. Our results show good correspondence to experimental data, phi-value and protection factor from H-D exchange experiments. The significance of conserved hydrophobic residues near F-value peaks for structural stability using hydrophobic packing is confirmed. Our prediction methods once again could extract a folding mechanism only knowing the amino acid sequence.
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Affiliation(s)
- Panyavut Aumpuchin
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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Sugita M, Matsuoka M, Kikuchi T. Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure. Proteins 2015; 83:1900-13. [PMID: 26248725 DOI: 10.1002/prot.24874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/23/2015] [Accepted: 07/29/2015] [Indexed: 11/09/2022]
Abstract
It has been suggested that proteins have substructures, called foldons, which can cooperatively fold into the native structure. However, several prior investigations define foldons in various ways, citing different foldon characteristics, thereby making the concept of a foldon ambiguous. In this study, we perform a Gō model simulation and analyze the characteristics of substructures that cooperatively fold into the native-like structure. Although some results do not agree well with the experimental evidence due to the simplicity of our coarse-grained model, our results strongly suggest that cooperatively folding units sometimes organize a partially overlapped and hierarchical structure. This view makes us easy to interpret some different proposal about the foldon as a difference of the hierarchical structure. On the basis of this finding, we present a new method to assign foldons and their hierarchy, using structural and sequence information. The results show that the foldons assigned by our method correspond to the intermediate structures identified by some experimental techniques. The new method makes it easy to predict whether a protein folds sequentially into the native structure or whether some foldons fold into the native structure in parallel.
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Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Masanari Matsuoka
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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Abstract
Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice (
Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the
nshb genes, consisting of
hb1,
hb2,
hb3,
hb4 and
hb5, and a single copy of the
thb gene exist in
Oryza sativa var. indica and
O.
sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O
2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O
2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O
2-transport, O
2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice
nshb and
thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice
nshbs and
thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the
cis-elements and
trans-acting factors that regulate the expression of rice
hb genes, and the partial understanding of the evolution of rice Hbs.
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Affiliation(s)
- Raúl Arredondo-Peter
- Laboratorio de Biofísica y Biología Molecular, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, 62210, Mexico
| | - Jose F Moran
- Instituto de Agrobiotecnología, IdAB-CSIC-Universidad Pública de Navarra-Gobierno de Navarra, Navarre, E-31192, Spain
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, University of Nebraska-Lincoln, Lincoln, NE, 68583-0937, USA
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Matsuoka M, Sugita M, Kikuchi T. Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures. BMC Res Notes 2014; 7:654. [PMID: 25231773 PMCID: PMC4180342 DOI: 10.1186/1756-0500-7-654] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. RESULTS It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. CONCLUSIONS The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.
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Affiliation(s)
| | | | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, Japan.
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Matsuoka M, Kikuchi T. Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins. BMC STRUCTURAL BIOLOGY 2014; 14:15. [PMID: 24884463 PMCID: PMC4055915 DOI: 10.1186/1472-6807-14-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/15/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND While some studies have shown that the 3D protein structures are more conservative than their amino acid sequences, other experimental studies have shown that even if two proteins share the same topology, they may have different folding pathways. There are many studies investigating this issue with molecular dynamics or Go-like model simulations, however, one should be able to obtain the same information by analyzing the proteins' amino acid sequences, if the sequences contain all the information about the 3D structures. In this study, we use information about protein sequences to predict the location of their folding segments. We focus on proteins with a ferredoxin-like fold, which has a characteristic topology. Some of these proteins have different folding segments. RESULTS Despite the simplicity of our methods, we are able to correctly determine the experimentally identified folding segments by predicting the location of the compact regions considered to play an important role in structural formation. We also apply our sequence analyses to some homologues of each protein and confirm that there are highly conserved folding segments despite the homologues' sequence diversity. These homologues have similar folding segments even though the homology of two proteins' sequences is not so high. CONCLUSION Our analyses have proven useful for investigating the common or different folding features of the proteins studied.
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Affiliation(s)
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan.
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9
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Matsuoka M, Fujita A, Kawai Y, Kikuchi T. Similar structures to the E-to-H helix unit in the globin-like fold are found in other helical folds. Biomolecules 2014; 4:268-88. [PMID: 24970216 PMCID: PMC4030988 DOI: 10.3390/biom4010268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 11/17/2022] Open
Abstract
A protein in the globin-like fold contains six alpha-helices, A, B, E, F, G and H. Among them, the E-to-H helix unit (E, F, G and H helices) forms a compact structure. In this study, we searched similar structures to the E-to-H helix of leghomoglobin in the whole protein structure space using the Dali program. Several similar structures were found in other helical folds, such as KaiA/RbsU domain and Type III secretion system domain. These observations suggest that the E-to-H helix unit may be a common subunit in the whole protein 3D structure space. In addition, the common conserved hydrophobic residues were found among the similar structures to the E-to-H helix unit. Hydrophobic interactions between the conserved residues may stabilize the 3D structures of the unit. We also predicted the possible compact regions of the units using the average distance method.
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Affiliation(s)
- Masanari Matsuoka
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
| | - Aoi Fujita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
| | - Yosuke Kawai
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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10
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Analysis of 3D structural differences in the IgG-binding domains based on the interresidue average-distance statistics. Amino Acids 2008; 35:541-9. [PMID: 18431532 DOI: 10.1007/s00726-008-0082-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 03/28/2008] [Indexed: 10/22/2022]
Abstract
It is well-known that the IgG-binding domain from staphylococcal protein A folds into a 3 alpha helix bundle structure, while the IgG-binding domain of streptococcal protein G forms an (alpha + beta) structure. Recently, He et al. (Biochemistry 44:14055-14061, 2005) made mutants of these proteins from the wild types of protein A and protein G strains. These mutants are referred to as protein A219 and protein G311, and it was showed that these two mutants have different 3D structures, i.e., the 3 alpha helix bundle structure and the (alpha + beta) structure, respectively, despite the high sequence identity (59%). The purpose of our study was to clarify how such 3D structural differences are coded in the sequences with high homology. To address this problem, we introduce a predicted contact map constructed based on the interresidue average-distance statistics for prediction of folding properties of a protein. We refer to this map as an average distance map (ADM). Furthermore, the statistics of interresidue distances can be converted to an effective interresidue potential. We calculated the contact frequency of each residue of a protein in random conformations with this effective interresidue potential, and then we obtained values similar to phi values. We refer to this contact frequency of each residue as a p(mu) value. The comparison of the p(mu) values to the phi values for a protein suggests that p(mu) values reveal the information on the folding initiation site. Using these techniques, we try to extract the information on the difference in the 3D structures of protein A219 and protein G311 coded in their amino acid sequences in the present work. The results show that the ADM analyses and the p(mu) value analyses predict the information of folding initiation sites, which can be used to detect the 3D difference in both proteins.
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Nakajima S, Kikuchi T. Analysis of the differences in the folding mechanisms of c-type lysozymes based on contact maps constructed with interresidue average distances. J Mol Model 2007; 13:587-94. [PMID: 17340112 DOI: 10.1007/s00894-007-0185-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2006] [Accepted: 02/06/2007] [Indexed: 10/23/2022]
Abstract
A method for analyzing differences in the folding mechanisms of proteins in the same family is presented. Using only information from the amino acid sequences, contact maps derived from the interresidue average distances are employed. These maps, referred to as average distance maps (ADM), are applied to the folding of c-type lysozymes. The results reveal that the ADMs of these lysozymes reflect the differences in the detailed folding mechanisms. Further possible applications of the present method are also discussed.
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Affiliation(s)
- Shunsuke Nakajima
- Department of Chemistry and Bioscience, College of Industrial Technology, Kurashiki University of Science and the Arts, Kurashiki, Okayama, Japan
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12
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Nakajima S, Alvarez-Salgado E, Kikuchi T, Arredondo-Peter R. Prediction of folding pathway and kinetics among plant hemoglobins using an average distance map method. Proteins 2006; 61:500-6. [PMID: 16184600 DOI: 10.1002/prot.20658] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Computational methods, such as the ADM (average distance map) method, have been developed to predict folding of homologous proteins. In this work we used the ADM method to predict the folding pathway and kinetics among selected plant nonsymbiotic (nsHb), symbiotic (Lb), and truncated (tHb) hemoglobins (Hbs). Results predicted that (1) folding of plant Hbs occurs throughout the formation of compact folding modules mostly formed by helices A, B, and C, and E, F, G, and H (folding modules A/C and E/H, respectively), and (2) primitive (moss) nsHbs fold in the C-->N direction, evolved (monocot and dicot) nsHbs fold either in the C-->N or N-->C direction, and Lbs and plant tHbs fold in the C-->N direction. We also predicted relative folding rates of plant Hbs from qualitative analyses of the stability of subdomains and classified plant Hbs into fast and moderate folding. ADM analysis of nsHbs predicted that prehelix A plays a role during folding of the N-terminal domain of Ceratodon nsHb, and that CD-loop plays a role in folding of primitive (Physcomitrella and Ceratodon) but not evolved nsHbs. Modeling of the rice Hb1 A/C and E/H modules showed that module E/H overlaps to the Mycobacterium tuberculosis HbO two-on-two folding. This observation suggests that module E/H is an ancient tertiary structure in plant Hbs.
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Affiliation(s)
- Shunsuke Nakajima
- Department of Bioscience and Bioinformatics, College of Information Science and Engineering, Ritsumeikan University, Shiga, Japan
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