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Song J. Molecular mechanisms of phase separation and amyloidosis of ALS/FTD-linked FUS and TDP-43. Aging Dis 2023:AD.2023.1118. [PMID: 38029395 DOI: 10.14336/ad.2023.1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023] Open
Abstract
FUS and TDP-43, two RNA-binding proteins from the heterogeneous nuclear ribonucleoprotein family, have gained significant attention in the field of neurodegenerative diseases due to their association with amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). They possess folded domains for binding ATP and various nucleic acids including DNA and RNA, as well as substantial intrinsically disordered regions (IDRs) including prion-like domains (PLDs) and RG-/RGG-rich regions. They play vital roles in various cellular processes, including transcription, splicing, microRNA maturation, RNA stability and transport and DNA repair. In particular, they are key components for forming ribonucleoprotein granules and stress granules (SGs) through homotypic or heterotypic liquid-liquid phase separation (LLPS). Strikingly, liquid-like droplets formed by FUS and TDP-43 may undergo aging to transform into less dynamic assemblies such as hydrogels, inclusions, and amyloid fibrils, which are the pathological hallmarks of ALS and FTD. This review aims to synthesize and consolidate the biophysical knowledge of the sequences, structures, stability, dynamics, and inter-domain interactions of FUS and TDP-43 domains, so as to shed light on the molecular mechanisms underlying their liquid-liquid phase separation (LLPS) and amyloidosis. The review further delves into the mechanisms through which ALS-causing mutants of the well-folded hPFN1 disrupt the dynamics of LLPS of FUS prion-like domain, providing key insights into a potential mechanism for misfolding/aggregation-prone proteins to cause neurodegenerative diseases and aging by gain of functions. With better understanding of different biophysical aspects of FUS and TDP-43, the ultimate goal is to develop drugs targeting LLPS and amyloidosis, which could mediate protein homeostasis within cells and lead to new treatments for currently intractable diseases, particularly neurodegenerative diseases such as ALS, FTD and aging. However, the study of membrane-less organelles and condensates is still in its infancy and therefore the review also highlights key questions that require future investigation.
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Effects of Selective Substitution of Cysteine Residues on the Conformational Properties of Chlorotoxin Explored by Molecular Dynamics Simulations. Int J Mol Sci 2019; 20:ijms20061261. [PMID: 30871150 PMCID: PMC6470725 DOI: 10.3390/ijms20061261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/10/2019] [Indexed: 12/27/2022] Open
Abstract
Chlorotoxin (CTX) is a 36–amino acid peptide with eight Cys residues that forms four disulfide bonds. It has high affinity for the glioma-specific chloride channel and matrix metalloprotease-2. Structural and binding properties of CTX analogs with various Cys residue substitutions with l-α-aminobutyric acid (Abu) have been previously reported. Using 4.2 µs molecular dynamics, we compared the conformational and essential space sampling of CTX and analogs with selective substitution of the Cys residues and associated disulfide bonds with either Abu or Ser. The native and substituted peptides maintained a high degree of α-helix propensity from residues 8 through 21, with the exception of substitution of the Cys5–Cys28 residues with Ser and the Cys16–Cys33 residues with Abu. In agreement with previous circular dichroism spectropolarimetry results, the C-terminal β-sheet content varied less from residues 25 through 29 and 32 through 36 and was well conserved in most analogs. The Cys16–Cys33 and Cys20–Cys35 disulfide-bonded residues appear to be required to maintain the αβ motif of CTX. Selective substitution with the hydrophilic Ser, may mitigate the destabilizing effect of Cys16–Cys33 substitution through the formation of an inter residue H-bond from Ser16:OγH to Ser33:OγH bridged by a water molecule. All peptides shared considerable sampled conformational space, which explains the retained receptor binding of the non-native analogs.
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Berkut AA, Usmanova DR, Peigneur S, Oparin PB, Mineev KS, Odintsova TI, Tytgat J, Arseniev AS, Grishin EV, Vassilevski AA. Structural similarity between defense peptide from wheat and scorpion neurotoxin permits rational functional design. J Biol Chem 2014; 289:14331-40. [PMID: 24671422 DOI: 10.1074/jbc.m113.530477] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In this study, we present the spatial structure of the wheat antimicrobial peptide (AMP) Tk-AMP-X2 studied using NMR spectroscopy. This peptide was found to adopt a disulfide-stabilized α-helical hairpin fold and therefore belongs to the α-hairpinin family of plant defense peptides. Based on Tk-AMP-X2 structural similarity to cone snail and scorpion potassium channel blockers, a mutant molecule, Tk-hefu, was engineered by incorporating the functionally important residues from κ-hefutoxin 1 onto the Tk-AMP-X2 scaffold. The designed peptide contained the so-called essential dyad of amino acid residues significant for channel-blocking activity. Electrophysiological studies showed that although the parent peptide Tk-AMP-X2 did not present any activity against potassium channels, Tk-hefu blocked Kv1.3 channels with similar potency (IC50 ∼ 35 μm) to κ-hefutoxin 1 (IC50 ∼ 40 μm). We conclude that α-hairpinins are attractive in their simplicity as structural templates, which may be used for functional engineering and drug design.
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Affiliation(s)
- Antonina A Berkut
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia, Moscow Institute of Physics and Technology (State University), Moscow 117303, Russia
| | - Dinara R Usmanova
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia, Moscow Institute of Physics and Technology (State University), Moscow 117303, Russia
| | - Steve Peigneur
- Laboratory of Toxicology and Pharmacology, University of Leuven, Leuven 3000, Belgium, and
| | - Peter B Oparin
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Konstantin S Mineev
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatyana I Odintsova
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Jan Tytgat
- Laboratory of Toxicology and Pharmacology, University of Leuven, Leuven 3000, Belgium, and
| | - Alexander S Arseniev
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Eugene V Grishin
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander A Vassilevski
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia,
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Incorporation of post-translational modified amino acids as an approach to increase both chemical and biological diversity of conotoxins and conopeptides. Amino Acids 2013; 46:125-51. [DOI: 10.1007/s00726-013-1606-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/17/2013] [Indexed: 02/06/2023]
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5
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Pichierri F. The electronic structure and dipole moment of charybdotoxin, a scorpion venom peptide with K+ channel blocking activity. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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6
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Jiang N, Ma J. Influence of Disulfide Connectivity, Electrostatics, and Hydrophobicity on the Conformational Variations of α-Conotoxin GI Single-Disulfide Analogues: Simulations with Polarizable Force Field. J Phys Chem B 2010; 114:11241-50. [DOI: 10.1021/jp102844h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nan Jiang
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, 210093, People’s Republic of China
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7
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Song J. Insight into "insoluble proteins" with pure water. FEBS Lett 2009; 583:953-9. [PMID: 19233178 DOI: 10.1016/j.febslet.2009.02.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 02/14/2009] [Accepted: 02/16/2009] [Indexed: 10/21/2022]
Abstract
Many proteins are not refoldable and also insoluble. Previously no general method was available to solubilize them and consequently their structural properties remained unknown. Surprisingly, we recently discovered that all insoluble proteins in our laboratory, which are highly diverse, can be solubilized in pure water. Structural characterization by CD and NMR led to their classification into three groups, all of which appear trapped in the highly disordered or partially-folded states with a substantial exposure of hydrophobic side chains. In this review, I discuss our results in a wide context and subsequently propose a model to rationalize the discovery. The potential applications are also explored in studying protein folding, design and membrane proteins.
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Affiliation(s)
- Jianxing Song
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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8
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Li M, Liu J, Ran X, Fang M, Shi J, Qin H, Goh JM, Song J. Resurrecting abandoned proteins with pure water: CD and NMR studies of protein fragments solubilized in salt-free water. Biophys J 2006; 91:4201-9. [PMID: 16980357 PMCID: PMC1635667 DOI: 10.1529/biophysj.106.093187] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many proteins expressed in Escherichia coli cells form inclusion bodies that are neither refoldable nor soluble in buffers. Very surprisingly, we recently discovered that all 11 buffer-insoluble protein fragments/domains we have, with a great diversity of cellular function, location, and molecular size, could be easily solubilized in salt-free water. The circular dichroism (CD) and NMR characterization led to classification of these proteins into three groups: group 1, with no secondary structure by CD and with narrowly-dispersed but sharp (1)H-(15)N heteronuclear single quantum correlation (HSQC) peaks; group 2, with secondary structure by CD but with HSQC peaks broadened and, consequently, only a small set of peaks detectable; and group 3, with secondary structure by CD and also well-separated HSQC peaks. Intriguingly, we failed to find any protein with a tight tertiary packing. Therefore, we propose that buffer-insoluble proteins may lack intrinsic ability to reach or/and to maintain a well-packed conformation, and thus are trapped in partially-folded states with many hydrophobic side chains exposed to the bulk solvent. As such, a very low ionic strength is sufficient to screen out intrinsic repulsive interactions and, consequently, allow the hydrophobic clustering/aggregation to occur. Marvelously enough, it appears that in pure water, proteins have the potential to manifest their full spectrum of structural states by utilizing intrinsic repulsive interactions to suppress the attractive hydrophobic clustering. Our discovery not only gives a novel insight into the properties of insoluble proteins, but also sheds the first light that we know of on previously unknown regimes associated with proteins.
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Affiliation(s)
- Minfen Li
- Department of Biological Sciences, Faculty of Science, Yong Loo Lin School of Mediciine, National Univeristy of Singapore, Singapore
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9
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Cheek S, Krishna SS, Grishin NV. Structural classification of small, disulfide-rich protein domains. J Mol Biol 2006; 359:215-37. [PMID: 16618491 DOI: 10.1016/j.jmb.2006.03.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 03/05/2006] [Accepted: 03/09/2006] [Indexed: 11/23/2022]
Abstract
Disulfide-rich domains are small protein domains whose global folds are stabilized primarily by the formation of disulfide bonds and, to a much lesser extent, by secondary structure and hydrophobic interactions. Disulfide-rich domains perform a wide variety of roles functioning as growth factors, toxins, enzyme inhibitors, hormones, pheromones, allergens, etc. These domains are commonly found both as independent (single-domain) proteins and as domains within larger polypeptides. Here, we present a comprehensive structural classification of approximately 3000 small, disulfide-rich protein domains. We find that these domains can be arranged into 41 fold groups on the basis of structural similarity. Our fold groups, which describe broader structural relationships than existing groupings of these domains, bring together representatives with previously unacknowledged similarities; 18 of the 41 fold groups include domains from several SCOP folds. Within the fold groups, the domains are assembled into families of homologs. We define 98 families of disulfide-rich domains, some of which include newly detected homologs, particularly among knottin-like domains. On the basis of this classification, we have examined cases of convergent and divergent evolution of functions performed by disulfide-rich proteins. Disulfide bonding patterns in these domains are also evaluated. Reducible disulfide bonding patterns are much less frequent, while symmetric disulfide bonding patterns are more common than expected from random considerations. Examples of variations in disulfide bonding patterns found within families and fold groups are discussed.
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Affiliation(s)
- Sara Cheek
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390, USA
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10
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Jia H, Bagherzadeh A, Hartzoulakis B, Jarvis A, Löhr M, Shaikh S, Aqil R, Cheng L, Tickner M, Esposito D, Harris R, Driscoll PC, Selwood DL, Zachary IC. Characterization of a bicyclic peptide neuropilin-1 (NP-1) antagonist (EG3287) reveals importance of vascular endothelial growth factor exon 8 for NP-1 binding and role of NP-1 in KDR signaling. J Biol Chem 2006; 281:13493-13502. [PMID: 16513643 DOI: 10.1074/jbc.m512121200] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neuropilin-1 (NP-1) is a receptor for vascular endothelial growth factor-A165 (VEGF-A165) in endothelial cells. To define the role of NP-1 in the biological functions of VEGF, we developed a specific peptide antagonist of VEGF binding to NP-1 based on the NP-1 binding site located in the exon 7- and 8-encoded VEGF-A165 domain. The bicyclic peptide, EG3287, potently (K(i) 1.2 microM) and effectively (>95% inhibition at 100 microM) inhibited VEGF-A165 binding to porcine aortic endothelial cells expressing NP-1 (PAE/NP-1) and breast carcinoma cells expressing only NP-1 receptors for VEGF-A, but had no effect on binding to PAE/KDR or PAE/Flt-1. Molecular dynamics calculations, a nuclear magnetic resonance structure of EG3287, and determination of stability in media, indicated that it constitutes a stable subdomain very similar to the corresponding region of native VEGF-A165. The C terminus encoded by exon 8 and the three-dimensional structure were both critical for EG3287 inhibition of NP-1 binding, whereas modifications at the N terminus had little effect. Although EG3287 had no direct effect on VEGF-A165 binding to KDR receptors, it inhibited cross-linking of VEGF-A165 to KDR in human umbilical vein endothelial cells co-expressing NP-1, and inhibited stimulation of KDR and PLC-gamma tyrosine phosphorylation, activation of ERKs1/2 and prostanoid production. These findings characterize the first specific antagonist of VEGF-A165 binding to NP-1 and demonstrate that NP-1 is essential for optimum KDR activation and intracellular signaling. The results also identify a key role for the C-terminal exon 8 domain in VEGF-A165 binding to NP-1.
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Affiliation(s)
- Haiyan Jia
- Centre for Cardiovascular Biology and Medicine, Department of Medicine, University College London, London WC1E 6JJ, United Kingdom; Ark Therapeutics Limited, The Rayne Institute, University College London, London WC1E 6JJ, United Kingdom
| | - Azadeh Bagherzadeh
- Centre for Cardiovascular Biology and Medicine, Department of Medicine, University College London, London WC1E 6JJ, United Kingdom; Ark Therapeutics Limited, The Rayne Institute, University College London, London WC1E 6JJ, United Kingdom
| | | | - Ashley Jarvis
- NCE Discovery Ltd., Cambridge CB4 0PA, United Kingdom
| | - Marianne Löhr
- Wolfson Institute for Biomedical Research, University College London, London WC1E GBT United Kingdom
| | | | - Rehan Aqil
- NCE Discovery Ltd., Cambridge CB4 0PA, United Kingdom
| | - Lili Cheng
- Centre for Cardiovascular Biology and Medicine, Department of Medicine, University College London, London WC1E 6JJ, United Kingdom; Ark Therapeutics Limited, The Rayne Institute, University College London, London WC1E 6JJ, United Kingdom
| | - Michelle Tickner
- Centre for Cardiovascular Biology and Medicine, Department of Medicine, University College London, London WC1E 6JJ, United Kingdom; Ark Therapeutics Limited, The Rayne Institute, University College London, London WC1E 6JJ, United Kingdom
| | - Diego Esposito
- Bloomsbury Centre for Structure Biology, Department of Biochemistry and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Richard Harris
- Bloomsbury Centre for Structure Biology, Department of Biochemistry and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Paul C Driscoll
- Bloomsbury Centre for Structure Biology, Department of Biochemistry and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - David L Selwood
- Wolfson Institute for Biomedical Research, University College London, London WC1E GBT United Kingdom
| | - Ian C Zachary
- Centre for Cardiovascular Biology and Medicine, Department of Medicine, University College London, London WC1E 6JJ, United Kingdom.
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11
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Wei Z, Song J. Molecular mechanism underlying the thermal stability and pH-induced unfolding of CHABII. J Mol Biol 2005; 348:205-18. [PMID: 15808864 DOI: 10.1016/j.jmb.2005.02.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 02/14/2005] [Accepted: 02/15/2005] [Indexed: 10/25/2022]
Abstract
The 37-residue alpha/beta protein CHABII was previously demonstrated to undergo a gradual pH-induced unfolding. It has been shown that even at pH 4.0 CHABII still retained a highly native-like secondary structure and tertiary topology although its tight side-chain packing was severely disrupted, typical of the molten globule state. Here, we have expressed and refolded the recombinant proteins of CHABII and its mutant [Phe21]-CHABII, and subsequently conducted extensive CD and NMR characterizations. The results indicated: (1) replacement of His21 by Phe in [Phe21]-CHABII eliminated the pH-induced unfolding from pH 6.5 to 4.0, indicating that His21 was responsible for the observed pH-induced unfolding of CHABII. Further examinations revealed that although the pH-induced unfolding of CHABII was also triggered by the protonation of the His residue as previously uncovered for apomyoglobin, their molecular mechanisms are different. (2) Monitoring the pH-induced unfolding by 1H-15N HSQC spectroscopy allowed us to visualize the gradual development of the CHABII molten globule. At pH 4.0, the HSQC spectrum of CHABII was poorly dispersed with dispersions of approximately 1 ppm over proton dimension and 10 ppm over 15N dimension, characteristic of severely or even "completely unfolded" proteins. One the other hand, unambiguous assignments of the NOESY spectra of CHABII led to the identification of the persistent medium and long-range NOEs at pH 4.0, which define a highly native-like secondary structure and tertiary packing. This implies that the degree of the native-like topology might be underestimated in the previous characterization of partially folded and even completely unfolded proteins. (3) Replacement of His21 by Phe with higher side-chain hydrophobicity only caused a minor structural rearrangement but considerably enhanced the packing interaction of the hydrophobic core, as evident from a dramatic increase in NOE contacts in [Phe21]-CHABII. The enhancement led to an increase of the thermal stability of [Phe21]-CHABII by approximately 17 deg. C.
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Affiliation(s)
- Zheng Wei
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge, Crescent, Singapore 119260
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12
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Ran X, Song J. Structural insight into the binding diversity between the Tyr-phosphorylated human ephrinBs and Nck2 SH2 domain. J Biol Chem 2005; 280:19205-12. [PMID: 15764601 DOI: 10.1074/jbc.m500330200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The binding interaction between the Nck2 SH2 domain and the phosphorylated ephrinB initiates a critical pathway for the reverse signaling network mediated by Eph receptor-ephrinB. Previously, the NMR structure and Tyr phosphorylations of the human ephrinB cytoplasmic domain have been studied. To obtain a complete story, it would be of significant interest to determine the structure of the Nck2 SH2 domain that shows a low sequence identity to other SH2 domains with known structures. Here, we report the determination of the solution structure of the human Nck2 SH2 domain and investigate its interactions with three phosphorylated ephrinB fragments by NMR spectroscopy. The results indicate that: 1) although the human Nck2 SH2 domain adopts a core tertiary fold common to all SH2 domains, it owns some unique properties such as a shorter C-terminal helix and unusual electrostatic potential surface. However, the most striking finding is that the C-terminal tail of the human Nck2 SH2 domain adopts a short antiparallel beta-sheet that, to the best of our knowledge, has never been identified in other SH2 domains. The truncation study suggests that one function of the C-terminal tail is to control the folding/solubility of the SH2 domain. 2) In addition to [Tyr(P)304]ephrinB2(301-322) and [Tyr(P)316]ephrinB2(301-322), here we identified [Tyr(P)330]ephrinB2(324-333) also capable of binding to the SH2 domain. The detailed NMR study indicated that the binding mechanisms for the three ephrinB fragments might be different. The binding with [Tyr(P)304]-ephrinB2(301-322) and [Tyr(P)316]ephrinB2(301-322) might be mostly involved in the residues over the N-half of the SH2 domain and provoked a significant increase in the backbone and side chain dynamics of the SH2 domain on the microsecond-millisecond time scale. In contrast, binding with [Tyr(P)330]ephrinB2(324-333) might have most residues over both halves engaged but induced less profound conformational dynamics on the mus-ms time scale.
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Affiliation(s)
- Xiaoyuan Ran
- Department of Biochemistry, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260
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Li M, Shi J, Wei Z, Teng FYH, Tang BL, Song J. Structural characterization of the human Nogo-A functional domains. Solution structure of Nogo-40, a Nogo-66 receptor antagonist enhancing injured spinal cord regeneration. ACTA ACUST UNITED AC 2004; 271:3512-22. [PMID: 15317586 DOI: 10.1111/j.0014-2956.2004.04286.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The recent discovery of the Nogo family of myelin inhibitors and the Nogo-66 receptor opens up a very promising avenue for the development of therapeutic agents for treating spinal cord injury. Nogo-A, the largest member of the Nogo family, is a multidomain protein containing at least two regions responsible for inhibiting central nervous system (CNS) regeneration. So far, no structural information is available for Nogo-A or any of its structural domains. We have subcloned and expressed two Nogo-A fragments, namely the 182 residue Nogo-A(567-748) and the 66 residue Nogo-66 in Escherichia coli. CD and NMR characterization indicated that Nogo-A(567-748) was only partially structured while Nogo-66 was highly insoluble. Nogo-40, a truncated form of Nogo-66, has been previously shown to be a Nogo-66 receptor antagonist that is able to enhance CNS neuronal regeneration. Detailed NMR examinations revealed that a Nogo-40 peptide had intrinsic helix-forming propensity, even in an aqueous environment. The NMR structure of Nogo-40 was therefore determined in the presence of the helix-stabilizing solvent trifluoroethanol. The solution structure of Nogo-40 revealed two well-defined helices linked by an unstructured loop, representing the first structure of Nogo-66 receptor binding ligands. Our results provide the first structural insights into Nogo-A functional domains and may have implications in further designs of peptide mimetics that would enhance CNS neuronal regeneration.
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Affiliation(s)
- Minfen Li
- Department of Biological Sciences, National University of Singapore, Singapore
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Shi J, Wei Z, Song J. Dissection study on the severe acute respiratory syndrome 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly specific protease inhibitors. J Biol Chem 2004; 279:24765-73. [PMID: 15037623 PMCID: PMC7982319 DOI: 10.1074/jbc.m311744200] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The severe acute respiratory syndrome (SARS) 3C-like protease consists of two distinct folds, namely the N-terminal chymotrypsin fold containing the domains I and II hosting the complete catalytic machinery and the C-terminal extra helical domain III unique for the coronavirus 3CL proteases. Previously the functional role of this extra domain has been completely unknown, and it was believed that the coronavirus 3CL proteases share the same enzymatic mechanism with picornavirus 3C proteases, which contain the chymotrypsin fold but have no extra domain. To understand the functional role of the extra domain and to characterize the enzyme-substrate interactions by use of the dynamic light scattering, circular dichroism, and NMR spectroscopy, we 1) dissected the full-length SARS 3CL protease into two distinct folds and subsequently investigated their structural and dimerization properties and 2) studied the structural and binding interactions of three substrate peptides with the entire enzyme and its two dissected folds. The results lead to several findings; 1) although two dissected parts folded into the native-like structures, the chymotrypsin fold only had weak activity as compared with the entire enzyme, and 2) although the chymotrypsin fold remained a monomer within a wide range of protein concentrations, the extra domain existed as a stable dimer even at a very low concentration. This observation strongly indicates that the extra domain contributes to the dimerization of the SARS 3CL protease, thus, switching the enzyme from the inactive form (monomer) to the active form (dimer). This discovery not only separates the coronavirus 3CL protease from the picornavirus 3C protease in terms of the enzymatic mechanism but also defines the dimerization interface on the extra helical domain as a new target for design of the specific protease inhibitors. Furthermore, the determination of the preferred solution conformation of the substrate peptide S1 together with the NMR differential line-broadening and transferred nuclear Overhauser enhancement study allows us to pinpoint the bound structure of the S1 peptide.
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Affiliation(s)
- Jiahai Shi
- Department of Biochemistry, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260
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15
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Flinn JP, Pallaghy PK, Lew MJ, Murphy R, Angus JA, Norton RS. Role of disulfide bridges in the folding, structure and biological activity of omega-conotoxin GVIA. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1434:177-90. [PMID: 10556572 DOI: 10.1016/s0167-4838(99)00165-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Omega-Conotoxin GVIA (GVIA), an N-type calcium channel blocker from the cone shell Conus geographus, is a 27 residue polypeptide cross-linked by three disulfide bonds. Here, we report the synthesis, structural analysis by (1)H NMR and bioassay of analogues of GVIA with disulfide bridge deletions and N- and C-terminal truncations. Two analogues that retain the crucial Lys-2 and Tyr-13 residues in loops constrained by two native disulfide bridges were synthesised using orthogonal protection of cysteine residues. In the first analogue, the Cys-15-Cys-26 disulfide bridge was deleted (by replacing the appropriate Cys residues with Ser), while in the second, this disulfide bridge and the eight C-terminal residues were deleted. No activity was detected for either analogue in a rat vas deferens assay, which measures N-type calcium channel activity in sympathetic nerve, and NMR studies showed that this was due to a gross loss of secondary and tertiary structure. Five inactive analogues that were synthesised without orthogonal protection of Cys residues as part of a previous study (Flinn et al. (1995) J. Pept. Sci. 1, 379-384) were also investigated. Three had single disulfide deletions (via Ser substitutions) and two had N- or C-terminal deletions in addition to the disulfide deletion. Peptide mapping and NMR analyses demonstrated that at least four of these analogues had non-native disulfide pairings, which presumably accounts for their lack of activity. The NMR studies also showed that all five analogues had substantially altered tertiary structures, although the backbone chemical shifts and nuclear Overhauser enhancements (NOEs) implied that native-like turn structures persisted in some of these analogues despite the non-native disulfide pairings. This work demonstrates the importance of the disulfides in omega-conotoxin folding and shows that the Cys-15-Cys-26 disulfide is essential for activity in GVIA. The NMR analyses also emphasise that backbone chemical shifts and short- and medium-range NOEs are dictated largely by local secondary structure elements and are not necessarily reliable monitors of the tertiary fold.
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Affiliation(s)
- J P Flinn
- Biomolecular Research Institute, 343 Royal Parade, Parkville, Vic., Australia
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Imperiali B, Ottesen JJ. Uniquely folded mini-protein motifs. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1999; 54:177-84. [PMID: 10517154 DOI: 10.1034/j.1399-3011.1999.00121.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mini-proteins containing fewer than 40 amino acids provide simple model systems for studying protein folding and stability as well as serving as scaffolds for the rational design of new functional motifs. This article reviews current progress on the design and characterization of discretely folded mini-protein motifs.
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Affiliation(s)
- B Imperiali
- Deapartment of Chemistry, Massachusetts, Institute of Technology, Cambridge 02139, USA
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Barnham KJ, Torres AM, Alewood D, Alewood PF, Domagala T, Nice EC, Norton RS. Role of the 6-20 disulfide bridge in the structure and activity of epidermal growth factor. Protein Sci 1998; 7:1738-49. [PMID: 10082370 PMCID: PMC2144085 DOI: 10.1002/pro.5560070808] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two synthetic analogues of murine epidermal growth factor, [Abu6, 20] mEGF4-48 (where Abu denotes amino-butyric acid) and [G1, M3, K21, H40] mEGF1-48, have been investigated by NMR spectroscopy. [Abu6, 20] mEGF4-48 was designed to determine the contribution of the 6-20 disulfide bridge to the structure and function of mEGF. The overall structure of this analogue was similar to that of native mEGF, indicating that the loss of the 6-20 disulfide bridge did not affect the global fold of the molecule. Significant structural differences were observed near the N-terminus, however, with the direction of the polypeptide chain between residues four and nine being altered such that these residues were now located on the opposite face of the main beta-sheet from their position in native mEGF. Thermal denaturation experiments also showed that the structure of [Abu6, 20] mEGF4-48 was less stable than that of mEGF. Removal of this disulfide bridge resulted in a significant loss of both mitogenic activity in Balb/c 3T3 cells and receptor binding on A431 cells compared with native mEGF and mEGF4-48, implying that the structural changes in [Abu6, 20] mEGF4-48, although limited to the N-terminus, were sufficient to interfere with receptor binding. The loss of binding affinity probably arose mainly from steric interactions of the dislocated N-terminal region with part of the receptor binding surface of EGF. [G1, M3, K21, H40] mEGF1-48 was also synthesized in order to compare the synthetic polypeptide with the corresponding product of recombinant expression. Its mitogenic activity in Balb/c 3T3 cells was similar to that of native mEGF and analysis of its 1H chemical shifts suggested that its structure was also very similar to native.
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Affiliation(s)
- K J Barnham
- Biomolecular Research Institute, Parkville, Victoria, Australia
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Lecomte C, Sabatier JM, Van Rietschoten J, Rochat H. Synthetic peptides as tools to investigate the structure and pharmacology of potassium channel-acting short-chain scorpion toxins. Biochimie 1998; 80:151-4. [PMID: 9587672 DOI: 10.1016/s0300-9084(98)80021-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In the last decade, numerous polypeptide toxins acting on ion channels have been isolated and characterized from diverse scorpion venoms. These toxins are useful pharmacological probes to study ion-specific channel proteins because they interact selectively with these channels and modulate their activities. Since low amounts of natural toxins can be isolated from scorpion venoms, the chemical synthesis approach is extremely useful to produce larger quantities of toxins and toxin analogs. This report is a succinct overview of the possibilities offered by the chemical synthesis to investigate pharmacological and structural properties of these compounds.
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Affiliation(s)
- C Lecomte
- Laboratoire de Biochimie, Ingéniérie des Protéines, CNRS UMR 6560, IFR Jean Roche, Faculté de Médecine Nord, Marseille, France
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