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Co-crystals of ethenzamide with 2-nitrobenzoic acid - Conformational analysis, MD simulations and DFT investigations. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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2
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Lu Z, Shi P, You H, Liu Y, Chen S. Transcriptomic analysis of the salivary gland of medicinal leech Hirudo nipponia. PLoS One 2018; 13:e0205875. [PMID: 30339694 PMCID: PMC6195274 DOI: 10.1371/journal.pone.0205875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022] Open
Abstract
Hirudo nipponia (known as Shui Zhi in Chinese) is a well-known Chinese medicine with numerous active ingredients in its body, especially in its saliva. This native Chinese blood-sucking leech has been used for therapeutic purposes since before 100 AD. Modern Chinese physicians use it for a wide range of diseases. Genomic data and molecular information about the pharmacologically active substances produced by this medicinal leech are presently unavailable despite this organism’s medicinal importance. In this study, we performed transcriptome profiling of the salivary glands of medicinal leech H. nipponia using the Illumina platform. In total, 84,657,362 clean reads were assembled into 50,535 unigenes. The obtained unigenes were compared to public databases. Furthermore, a unigene sequence similarity search and comparisons with the whole transcriptome of medical leech were performed to identify potential proteins. Finally, more than 21 genes were predicted to be involved in anticoagulatory, antithrombotic, antibacterial, anti-inflammatory and antitumor processes, which might play important roles in the treatment of various diseases. This study is the first analysis of a sialotranscriptome in H. nipponia. The transcriptome profile will shed light on its genetic background and provide a useful tool to deepen our understanding of the medical value of H. nipponia.
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Affiliation(s)
- Zenghui Lu
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Ping Shi
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Huajian You
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Yanqi Liu
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Shijiang Chen
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
- * E-mail:
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Uversky VN. Flexibility of the "rigid" classics or rugged bottom of the folding funnels of myoglobin, lysozyme, RNase A, chymotrypsin, cytochrome c, and carboxypeptidase A1. INTRINSICALLY DISORDERED PROTEINS 2018; 5:e1355205. [PMID: 30250772 DOI: 10.1080/21690707.2017.1355205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/08/2017] [Indexed: 10/18/2022]
Abstract
The abilities to crystalize of a globular protein and to solve its crystal structure seem to represent triumph of the lock-and-key model of protein functionality, where the presence of unique 3D structure resembling aperiodic crystal is considered as a prerequisite for a given protein to possess specific biologic activity. The history of protein crystallography has its roots in first crystal structures of myoglobin, lysozyme, RNase A, chymotrypsin, cytochrome c, and carboxypeptidase A1 solved more than 50 y ago. This article briefly considers extensive structural information currently available for these proteins and shows that the bottoms of their folding funnels (i.e., the lowest parts of their potential energy landscapes) are not smoothed but rugged. In other words, these crystallization classics are characterized by significant conformational flexibility and are not rigid (immobile) crystal-like entities.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
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Abstract
The correct balance between proteases and their natural protein inhibitors is of great importance in living systems. Protease inhibitors usually comprise small folds that are crosslinked by a high number of disulfide bonds, making them perfect models for the study of oxidative folding. To date, the oxidative folding of numerous protease inhibitors has been analyzed, revealing a great diversity of folding pathways that differ mainly in the heterogeneity and native disulfide-bond content of their intermediates. The two extremes of this diversity are represented by bovine pancreatic trypsin inhibitor and hirudin, which fold, respectively, via few native intermediates and heterogeneous scrambled isomers. Other proteins, such as leech carboxypeptidase inhibitor, share characteristics of both models displaying mixed folding pathways. The study of the oxidative folding of two-domain inhibitors, such as secretory leukocyte protease inhibitor, tick carboxypeptidase inhibitor, and Ascaris carboxypeptidase inhibitor, has provided some clues about how two-domain protease inhibitors may fold, that is, either by folding each domain autonomously or with one domain assisting in the folding of the other. Finally, the recent determination of the structures of the major intermediates of protease inhibitors has shed light on the molecular mechanisms guiding the oxidative folding of small disulfide-rich proteins.
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Affiliation(s)
- Joan L Arolas
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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Gross G, Gallopin M, Vandame M, Couprie J, Stura E, Zinn-Justin S, Drevet P. Conformational exchange is critical for the productivity of an oxidative folding intermediate with buried free cysteines. J Mol Biol 2010; 403:299-312. [PMID: 20804768 DOI: 10.1016/j.jmb.2010.07.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 07/23/2010] [Accepted: 07/26/2010] [Indexed: 11/16/2022]
Abstract
Much has been learned about the folding of proteins from comparative studies of the folding of proteins that are related in sequence and structure. Observation of the effects of mutations helps account for sequence-specific properties and large variations in folding rates observed in homologous proteins, which are not explained by structure-derived descriptions. The folding kinetics of variants of a β-stranded protein, toxin α from Naja nigricollis, depends on the length of their loop lk1. These proteins, named Tox60, Tox61, and Tox62, contain four disulfide bonds. We show that their oxidative refolding pathways are similar. Differences in these pathways are restricted to the last step of the reaction, that is, the closure of the last disulfide. At this step, two species of three-disulfide intermediates are observed: intermediate C lacking the B3 disulfide and intermediate D lacking the B2 disulfide. Surprisingly, D is the most productive intermediate for Tox61 despite the low accessibility of its free cysteines. However, in the case of Tox62, its conversion efficiency drops by 2 orders of magnitude and C becomes the most productive intermediate. NMR was used in order to study the structural dynamics of each of these intermediates. Both three-disulfide intermediates of Tox61 exist in two forms, exchanging on the 1- to 100-ms scale. One of these forms is structurally very close to the native Tox61, whereas the other is always significantly more flexible on a picosecond-to-nanosecond timescale. On the other hand, in the case of Tox62, the three-disulfide intermediates only show a native-like structure. The higher conformational heterogeneity of Tox61 intermediate D allows an increased accessibility of its free cysteines to oxidative agents, which explains its faster native disulfide formation. Thus, residue deletion in loop lk1 probably abrogates stabilizing intramolecular interactions, creates conformational heterogeneity, and increases the folding rate of Tox60 and Tox61 compared to Tox62.
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Affiliation(s)
- Gregori Gross
- CEA/DSV/iBiTEC-S/SBIGeM, F-91191 Gif sur Yvette Cedex, France
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Arolas JL, Castillo V, Bronsoms S, Aviles FX, Ventura S. Designing Out Disulfide Bonds of Leech Carboxypeptidase Inhibitor: Implications for Its Folding, Stability and Function. J Mol Biol 2009; 392:529-46. [DOI: 10.1016/j.jmb.2009.06.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 05/04/2009] [Accepted: 06/18/2009] [Indexed: 11/26/2022]
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The structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot protein. Structure 2008; 16:842-51. [PMID: 18547517 DOI: 10.1016/j.str.2008.02.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Revised: 01/16/2008] [Accepted: 02/19/2008] [Indexed: 11/24/2022]
Abstract
We have determined the three-dimensional structure of a two-disulfide intermediate (Cys(8)-Cys(20), Cys(14)-Cys(26)) on the oxidative folding pathway of the cyclotide MCoTI-II. Cyclotides have a range of bioactivities and, because of their exceptional stability, have been proposed as potential molecular scaffolds for drug design applications. The three-dimensional structure of the stable two-disulfide intermediate shows for the most part identical secondary and tertiary structure to the native state. The only exception is a flexible loop, which is collapsed onto the protein core in the native state, whereas in the intermediate it is more loosely associated with the remainder of the protein. The results suggest that the native fold of the peptide does not represent the free energy minimum in the absence of the Cys(1)-Cys(18) disulfide bridge and that although there is not a large energy barrier, the peptide must transiently adopt an energetically unfavorable state before the final disulfide can form.
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Abstract
Comprehensive understanding of the mechanism of protein folding requires the elucidation of both a folding pathway and a folding model. This entails characterization of the properties and structures of folding intermediates populated along the folding pathway, as well as the formation and interplay of secondary structures and tertiary structures along the course of folding. Using the conventional unfolding-refolding technique, there are limitations of acquiring these data in detail because of the inherent difficulty of trapping and analysis of folding intermediates. The technique of oxidative folding, in contrast, permits trapping, isolation, and further structural characterization of folding intermediates at any stage of the folding process. In this brief review, we present the potential of the technique of oxidative folding for concurrent analysis of both folding pathways and folding models.
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Affiliation(s)
- Jui-Yoa Chang
- Research Center for Protein Chemistry, Brown Foundation Institute of Molecular Medicine, Department of Biochemistry and Molecular Biology, University of Texas, Houston, Texas 77030, USA.
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Salamanca S, Chang JY. Pathway of oxidative folding of a 3-disulfide alpha-lactalbumin may resemble either BPTI model or hirudin model. Protein J 2007; 25:275-87. [PMID: 16710754 DOI: 10.1007/s10930-006-9011-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pathways of oxidative folding of disulfide proteins display a high degree of diversity and vary among two extreme models. The BPTI model is defined by limited species of folding intermediates adopting mainly native disulfide bonds. The hirudin model is characterized by highly heterogeneous folding intermediates containing mostly non-native disulfide bonds. alphaLA-IIIA is a 3-disulfide variant of alpha-lactalbumin (alphaLA) with a 3-D conformation essentially identical to that of intact alphaLA. alphaLA-IIIA contains 3 native disulfide bonds of alphaLA, two of them are located at the calcium binding beta-subdomain (Cys61-Cys77 and Cys73-Cys91) and the third bridge is located within the alpha-helical domain of the molecule (Cys28-Cys111). We investigate here the pathway of oxidative folding of fully reduced alphaLA-IIIA with and without stabilization of its beta-subdomain by calcium binding. In the absence of calcium, the folding pathway of alphaLA-IIIA was shown to resemble that of hirudin model. Upon stabilization of beta-sheet domain by calcium binding, the folding pathway of alphaLA-IIIA exhibits a striking similarity to that of BPTI model. Three predominant folding intermediates of alphaLA-IIIA containing exclusively native disulfide bonds were isolated and structurally characterized. Our results further demonstrate that stabilization of subdomains in a protein may dictate its folding pathway and represent a major cause for the existing diversity in the folding pathways of the disulfide-containing proteins.
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Affiliation(s)
- Silvia Salamanca
- Research Center for Protein Chemistry, Institute of Molecular Medicine, 2121 W. Holcombe Blvd., Houston, TX 77030, USA
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Arolas JL, Aviles FX, Chang JY, Ventura S. Folding of small disulfide-rich proteins: clarifying the puzzle. Trends Biochem Sci 2006; 31:292-301. [PMID: 16600598 DOI: 10.1016/j.tibs.2006.03.005] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Revised: 02/20/2006] [Accepted: 03/22/2006] [Indexed: 11/21/2022]
Abstract
The process by which small proteins fold to their native conformations has been intensively studied over the past few decades. The particular chemistry of disulfide-bond formation has facilitated the characterization of the oxidative folding of numerous small, disulfide-rich proteins with results that illustrate a high level of diversity in folding mechanisms, differing in the heterogeneity and native disulfide-bond content of their intermediates. Information from folding studies of these proteins, together with the recent structural determinations of predominant intermediates, has provided new molecular insights into oxidative folding and clarifies the major rules that govern it.
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Affiliation(s)
- Joan L Arolas
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona; 08193 Bellaterra, Barcelona, Spain
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Lu BY, Jiang C, Chang JY. Isomers of Epidermal Growth Factor with Ser ⇒ Cys Mutation at the N-Terminal Sequence: Isomerization, Stability, Unfolding, Refolding, and Structure. Biochemistry 2005; 44:15032-41. [PMID: 16274250 DOI: 10.1021/bi051399c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of human epidermal growth factor (EGF, 53 amino acids) comprises three distinct loops (A, B, and C) connected correspondingly by the three native disulfide bonds, Cys(6)-Cys(20), Cys(14)-Cys(31), and Cys(33)-Cys(42). The connection of Cys(6) and Cys(20) forming the N-terminal A loop is essential for the biological activity of EGF [Barnham et al. (1998) Protein Sci. 7, 1738-1749] and has also been shown to represent a major kinetic trap in the oxidative folding of EGF [Chang et al. (2001) J. Biol. Chem. 276, 4845-4852]. To further understand the chemical nature of this kinetic trap, we have prepared three EGF mutants each with a single Ser --> Cys mutation at Ser residues (Ser(2), Ser(4), and Ser(9)) flanking Cys(6). This allows competition between Cys(6) and mutated Cys(2), Cys(4), and Cys(9) to link with Cys(20) and to form EGF isomers containing different sizes of the A loop. The results show that, in the cases of EGF(S2C) and EGF(S4C), native Cys(6)-Cys(20) is favored over Cys(2)-Cys(20) and Cys(4)-Cys(20) by 4.5- and 9-fold, respectively, in the state of equilibrium. However, in the case of EGF(S9C), a non-native Cys(9)-Cys(20) is thermodynamically more stable than the native Cys(6)-Cys(20) by a free-energy difference (DeltaG degrees ) of 1.12 kcal/mol. Implications of these data in the formation of kinetic trap of EGF folding are discussed. Stabilized isomers of EGF were further generated from denaturation of wild-type and mutant EGF via the method of disulfide scrambling. Properties of these diverse isomers of EGF, including their isomerization, stability, unfolding, refolding, and disulfide structures, are described in this paper.
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Affiliation(s)
- Bao-Yuan Lu
- Research Center for Protein Chemistry, Institute of Molecular Medicine, The University of Texas, Houston, Texas 77030, USA
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