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Paoletti F. ATP binding to Nerve Growth Factor (NGF) and pro-Nerve Growth Factor (proNGF): an endogenous molecular switch modulating neurotrophins activity. Biochem Soc Trans 2024; 52:1293-1304. [PMID: 38716884 DOI: 10.1042/bst20231089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/27/2024]
Abstract
ATP has recently been reconsidered as a molecule with functional properties which go beyond its recognized role of the energetic driver of the cell. ATP has been described as an allosteric modulator as well as a biological hydrotrope with anti-aggregation properties in the crowded cellular environment. The role of ATP as a modulator of the homeostasis of the neurotrophins (NTs), a growth factor protein family whose most known member is the nerve growth factor (NGF), has been investigated. The modulation of NTs by small endogenous ligands is still a scarcely described area, with few papers reporting on the topic, and very few reports on the molecular determinants of these interactions. However, a detailed atomistic description of the NTs interaction landscape is of urgent need, aiming at the identification of novel molecules as potential therapeutics and considering the wide range of potential pharmacological applications for NGF and its family members. This mini-review will focus on the unique cartography casting the interactions of the endogenous ligand ATP, in the interaction with NGF as well as with its precursor proNGF. These interactions revealed interesting features of the ATP binding and distinct differences in the binding mode between the highly structured mature NGF and its precursor, proNGF, which is characterized by an intrinsically unstructured domain. The overview on the recent available data will be presented, together with the future perspectives on the field.
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Affiliation(s)
- Francesca Paoletti
- Institute of Crystallography - C.N.R. - Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
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2
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Pham TL, Thomas F. Design of Functional Globular β-Sheet Miniproteins. Chembiochem 2024; 25:e202300745. [PMID: 38275210 DOI: 10.1002/cbic.202300745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
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Affiliation(s)
- Truc Lam Pham
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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3
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Prakash V, Ranbhor R, Ramakrishnan V. De Novo Designed Heterochiral Blue Fluorescent Protein. ACS OMEGA 2020; 5:26382-26388. [PMID: 33110966 PMCID: PMC7581079 DOI: 10.1021/acsomega.0c02574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/24/2020] [Indexed: 05/08/2023]
Abstract
Diversification of chain stereochemistry offers a tremendous increase in protein design space. We have designed a minimal fluorescent protein, pregnant with β-(1-azulenyl)-l-alanine in the hydrophobic core of a heterotactic protein scaffold, employing automated design tools such as automated repetitive simulated annealing molecular dynamics and IDeAS. The de novo designed heterochiral protein can be selectively excited at 342 nm, quite distant from the intrinsic fluorophore, and emits in the blue region. The structure and stability of the designed proteins were evaluated by established spectroscopic and calorimetric methods.
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Affiliation(s)
- Vivek Prakash
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
| | - Ranjit Ranbhor
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Mumbai 400076, India
| | - Vibin Ramakrishnan
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
- . Phone: +91-361-258-2227
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Belwal VK, Datta D, Chaudhary N. The β‐turn‐supporting motif in the polyglutamine binding peptide QBP1 is essential for inhibiting huntingtin aggregation. FEBS Lett 2020; 594:2894-2903. [DOI: 10.1002/1873-3468.13873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Vinay Kumar Belwal
- Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati India
| | - Debika Datta
- Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati India
| | - Nitin Chaudhary
- Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati India
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5
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Mompeán M, Hervás R, Xu Y, Tran TH, Guarnaccia C, Buratti E, Baralle F, Tong L, Carrión-Vázquez M, McDermott AE, Laurents DV. Structural Evidence of Amyloid Fibril Formation in the Putative Aggregation Domain of TDP-43. J Phys Chem Lett 2015; 6:2608-15. [PMID: 26266742 PMCID: PMC5568655 DOI: 10.1021/acs.jpclett.5b00918] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
TDP-43 can form pathological proteinaceous aggregates linked to ALS and FTLD. Within the putative aggregation domain, engineered repeats of residues 341-366 can recruit endogenous TDP-43 into aggregates inside cells; however, the nature of these aggregates is a debatable issue. Recently, we showed that a coil to β-hairpin transition in a short peptide corresponding to TDP-43 residues 341-357 enables oligomerization. Here we provide definitive structural evidence for amyloid formation upon extensive characterization of TDP-43(341-357) via chromophore and antibody binding, electron microscopy (EM), solid-state NMR, and X-ray diffraction. On the basis of these findings, structural models for TDP-43(341-357) oligomers were constructed, refined, verified, and analyzed using docking, molecular dynamics, and semiempirical quantum mechanics methods. Interestingly, TDP-43(341-357) β-hairpins assemble into a novel parallel β-turn configuration showing cross-β spine, cooperative H-bonding, and tight side-chain packing. These results expand the amyloid foldome and could guide the development of future therapeutics to prevent this structural conversion.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física Rocasolano, CSIC Serrano 119, 28006 Madrid, Spain
- Corresponding Authors: (M.M.) Tel: +34 91-745-9543. Fax: +34 91-564-2431. . (D.V.L.)
| | - Rubén Hervás
- Instituto Cajal, CSIC Avda, Doctor Arce 37, E-28002 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Crta. de Cantoblanco no. 8, E-28049 Cantoblanco, Madrid, Spain
| | - Yunyao Xu
- Department of Chemistry, Columbia University, 344 Havemeyer Hall, New York, New York 10027, United States
| | - Timothy H. Tran
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Francisco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Mariano Carrión-Vázquez
- Instituto Cajal, CSIC Avda, Doctor Arce 37, E-28002 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Crta. de Cantoblanco no. 8, E-28049 Cantoblanco, Madrid, Spain
| | - Ann E. McDermott
- Department of Chemistry, Columbia University, 344 Havemeyer Hall, New York, New York 10027, United States
| | - Douglas V. Laurents
- Instituto de Química Física Rocasolano, CSIC Serrano 119, 28006 Madrid, Spain
- Corresponding Authors: (M.M.) Tel: +34 91-745-9543. Fax: +34 91-564-2431. . (D.V.L.)
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Ramos-Martín F, Hervás R, Carrión-Vázquez M, Laurents DV. NMR spectroscopy reveals a preferred conformation with a defined hydrophobic cluster for polyglutamine binding peptide 1. Arch Biochem Biophys 2014; 558:104-10. [PMID: 25009140 DOI: 10.1016/j.abb.2014.06.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/20/2014] [Accepted: 06/21/2014] [Indexed: 11/16/2022]
Abstract
Several important human inherited neurodegenerative diseases are caused by "polyQ expansions", which are aberrant long repeats of glutamine residues in proteins. PolyQ binding peptide 1 (QBP1), whose minimal active core sequence is Trp-Lys-Trp-Trp-Pro-Gly-Ile-Phe, binds to expanded polyQs and blocks their β-structure transition, aggregation and in vivo neurodegeneration. Whereas QBP1 is a widely used, commercially available product, its structure is unknown. Here, we have characterized the conformations of QBP1 and a scrambled peptide (Trp-Pro-Ile-Trp-Lys-Gly-Trp-Phe) in aqueous solution by CD, fluorescence and NMR spectroscopies. A CD maximum at 227 nm suggests the presence of rigid Trp side chains in QBP1. Based on 41 NOE-derived distance constraints, the 3D structure of QBP1 was determined. The side chains of Trp 4 and Ile 7, and to a lesser extent, those of Lys 2, Trp 3 and Phe 8, form a small hydrophobic cluster. Pro 5 and Gly 6 adopt a type II tight turn and Lys 2's ζ-NH3(+) is positioned to form a favorable cation-π interaction with Trp 4's indole ring. In contrast, the scrambled QBP1 peptide, which lacks inhibitory activity, does not adopt a preferred structure. These results provide a basis for future structure-based design approaches to further optimize QBP1 for therapy.
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Affiliation(s)
- Francisco Ramos-Martín
- Instituto Cajal, IC-Consejo Superior de Investigaciones Científicas, Avda. Doctor Arce 37, E-28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), E-28049 Cantoblanco, Madrid, Spain
| | - Rubén Hervás
- Instituto Cajal, IC-Consejo Superior de Investigaciones Científicas, Avda. Doctor Arce 37, E-28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), E-28049 Cantoblanco, Madrid, Spain
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-Consejo Superior de Investigaciones Científicas, Avda. Doctor Arce 37, E-28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), E-28049 Cantoblanco, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid E-28006, Spain.
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