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Kalitnik A, Szefczyk M, Wojciechowska AW, Wojciechowski JW, Gąsior-Głogowska M, Olesiak-Bańska J, Kotulska M. Cytotoxic Staphylococcus aureus PSMα3 inhibits the aggregation of human insulin in vitro. Phys Chem Chem Phys 2024; 26:15587-15599. [PMID: 38757742 DOI: 10.1039/d4cp00669k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Phenol-soluble modulins (PSMs) are extracellular short amphipathic peptides secreted by the bacteria Staphylococcus aureus (S. aureus). They play an essential role in the bacterial lifecycle, biofilm formation, and stabilisation. From the PSM family, PSMα3 has been of special interest recently due to its cytotoxicity and highly stable α-helical conformation, which also remains in its amyloid fibrils. In particular, PSMα3 fibrils were shown to be composed of self-associating "sheets" of α-helices oriented perpendicular to the fibril axis, mimicking the architecture of canonical cross-β fibrils. Therefore, they were called cross-α-fibrils. PSMα3 was synthesised and verified for identity with wild-type sequences (S. aureus). Then, using several experimental techniques, we evaluated its propensity for in vitro aggregation. According to our findings, synthetic PSMα3 (which lacks the N-terminal formyl groups found in bacteria) does not form amyloid fibrils and maintains α-helical conformation in a soluble monomeric form for several days of incubation. We also evaluated the influence of PSMα3 on human insulin fibrillation in vitro, using a variety of experimental approaches in combination with computational molecular studies. First, it was shown that PSMα3 drastically inhibits the fibrillation of human insulin. The anti-fibrillation effect of PSMα3 was concentration-dependent and required a concentration ratio of PSMα3: insulin equal to or above 1 : 100. Molecular modelling revealed that PSMα3 most likely inhibits the production of insulin primary nuclei by competing for residues involved in its dimerization.
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Affiliation(s)
- Aleksandra Kalitnik
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Alicja W Wojciechowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Joanna Olesiak-Bańska
- Institute of Advanced Materials, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Małgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
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2
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Martin WJ, McClelland LJ, Nold SM, Boshae KL, Bowler BE. Effect of proline content and histidine ligation on the dynamics of Ω-loop D and the peroxidase activity of iso-1-cytochrome c. J Inorg Biochem 2024; 252:112474. [PMID: 38176365 DOI: 10.1016/j.jinorgbio.2023.112474] [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: 10/16/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
To study how proline residues affect the dynamics of Ω-loop D (residues 70 to 85) of cytochrome c, we prepared G83P and G83A variants of yeast iso-1-cytochrome c (iso-1-Cytc) in the presence and absence of a K73H mutation. Ω-loop D is important in controlling both the electron transfer function of Cytc and the peroxidase activity of Cytc used in apoptosis because it provides the Met80 heme ligand. The G83P and G83A mutations have no effect on the global stability of iso-1-Cytc in presence or absence of the K73H mutation. However, both mutations destabilize the His73-mediated alkaline conformer relative to the native state. pH jump stopped-flow experiments show that the dynamics of the His73-mediated alkaline transition are significantly enhanced by the G83P mutation. Gated electron transfer studies show that the enhanced dynamics result from an increased rate of return to the native state, whereas the rate of loss of Met80 ligation is unchanged by the G83P mutation. Thus, the G83P substitution does not stiffen the conformation of the native state. Because bis-His heme ligation occurs when Cytc binds to cardiolipin-containing membranes, we studied the effect of His73 ligation on the peroxidase activity of Cytc, which acts as an early signal in apoptosis by causing oxygenation of cardiolipin. We find that the His73 alkaline conformer suppresses the peroxidase activity of Cytc. Thus, the bis-His ligated state of Cytc formed upon binding to cardiolipin is a negative effector for the peroxidase activity of Cytc early in apoptosis.
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Affiliation(s)
- William J Martin
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Levi J McClelland
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Division of Biological Sciences, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Shiloh M Nold
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Kassandra L Boshae
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Bruce E Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States.
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3
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Škrbić T, Giacometti A, Hoang TX, Maritan A, Banavar JR. A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures. Polymers (Basel) 2024; 16:502. [PMID: 38399880 PMCID: PMC10892082 DOI: 10.3390/polym16040502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Linear chain molecules play a central role in polymer physics with innumerable industrial applications. They are also ubiquitous constituents of living cells. Here, we highlight the similarities and differences between two distinct ways of viewing a linear chain. We do this, on the one hand, through the lens of simulations for a standard polymer chain of tethered spheres at low and high temperatures and, on the other hand, through published experimental data on an important class of biopolymers, proteins. We present detailed analyses of their local and non-local structures as well as the maps of their closest contacts. We seek to reconcile the startlingly different behaviors of the two types of chains based on symmetry considerations.
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Affiliation(s)
- Tatjana Škrbić
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, 30170 Venice, Italy;
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, OR 97403, USA;
| | - Achille Giacometti
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, 30170 Venice, Italy;
- European Centre for Living Technology (ECLT), Ca’ Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Trinh X. Hoang
- Institute of Physics, Vietnam Academy of Science and Technology, Hanoi 11108, Vietnam;
| | - Amos Maritan
- Department of Physics and Astronomy, University of Padua, 35122 Padua, Italy;
| | - Jayanth R. Banavar
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, OR 97403, USA;
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4
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Purbaya S, Harneti D, Safriansyah W, Rahmawati, Wulandari AP, Mulyani Y, Supratman U. Secondary Metabolites of Biscogniauxia: Distribution, Chemical Diversity, Bioactivity, and Implications of the Occurrence. Toxins (Basel) 2023; 15:686. [PMID: 38133190 PMCID: PMC10747060 DOI: 10.3390/toxins15120686] [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: 09/30/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023] Open
Abstract
The genus Biscogniauxia, a member of the family Xylariaceae, is distributed worldwide with more than 50 recognized taxa. Biscogniauxia species is known as a plant pathogen, typically acting as a parasite on tree bark, although certain members of this genus also function as endophytic microorganisms. Biscogniauxia endophytic strain has received attention in many cases, which includes constituent research leading to the discovery of various bioactive secondary metabolites. Currently, there are a total of 115 chemical compounds belonging to the class of secondary metabolites, and among these compounds, fatty acids have been identified. In addition, the strong pharmacological agents of this genus are (3aS,4aR,8aS,9aR)-3a-hydroxy-8a-methyl-3,5-dimethylenedecahydronaphto [2,3-b]furan-2(3H)-one (HDFO) (antifungal), biscopyran (phytotoxic activity), reticulol (antioxidant), biscogniazaphilone A and B (antimycobacterial), and biscogniauxone (Enzyme GSK3 inhibitor). This comprehensive research contributes significantly to the potential discovery of novel drugs produced by Biscogniauxia and holds promise for future development. Importantly, it represents the first-ever review of natural products originating from the Biscogniauxia genus.
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Affiliation(s)
- Sari Purbaya
- Department of Chemistry, Faculty of Science and Informatics, Universitas Jenderal Achmad Yani, Cimahi 40531, Indonesia;
- Departments of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (D.H.); (W.S.); (Y.M.)
| | - Desi Harneti
- Departments of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (D.H.); (W.S.); (Y.M.)
| | - Wahyu Safriansyah
- Departments of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (D.H.); (W.S.); (Y.M.)
| | - Rahmawati
- Central Laboratory, Universitas Padjadjaran, Jatinangor 45363, Indonesia;
| | - Asri Peni Wulandari
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia;
| | - Yeni Mulyani
- Departments of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (D.H.); (W.S.); (Y.M.)
| | - Unang Supratman
- Departments of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, Indonesia; (D.H.); (W.S.); (Y.M.)
- Central Laboratory, Universitas Padjadjaran, Jatinangor 45363, Indonesia;
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5
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Caramiello A, Bellucci MC, Marti-Rujas J, Sacchetti A, Volonterio A. Turn-Mimic Hydantoin-Based Loops Constructed by a Sequential Multicomponent Reaction. J Org Chem 2023; 88:15790-15804. [PMID: 37932902 PMCID: PMC10661056 DOI: 10.1021/acs.joc.3c01861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/08/2023]
Abstract
A collection of peptidomimetics characterized by having an aspartic acid motif embedded in a rigid hydantoin heterocycle are synthesized through a sequential multicomponent domino process followed by standard regioselective deprotection/coupling reactions based on acid-base liquid/liquid purification protocols. 1H nuclear magnetic resonance experiments, molecular modeling, and X-ray analysis showed that the resulting hydantoin-based loops I (in particular) and II (to a lesser extent) can be considered novel β-turn inducer motifs being able to project two peptide-like strands in a U-shaped conformation driven by the formation of intermolecular hydrogen bonds.
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Affiliation(s)
- Alessio
Maria Caramiello
- Department
of Chemistry, Material and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, Milano 20133, Italy
| | - Javier Marti-Rujas
- Department
of Chemistry, Material and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Alessandro Sacchetti
- Department
of Chemistry, Material and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Material and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
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6
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Hazra MK, Gilron Y, Levy Y. Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction. J Mol Biol 2023; 435:168196. [PMID: 37442414 DOI: 10.1016/j.jmb.2023.168196] [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: 03/25/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Intrinsically disordered proteins (IDPs) adopt a wide array of different conformations that can be constrained by the presence of proline residues, which are frequently found in IDPs. To assess the effects of proline, we designed a series of peptides that differ with respect to the number of prolines in the sequence and their organization. Using high-resolution atomistic molecular dynamics simulations, we found that accounting for whether the proline residues are clustered or isolated contributed significantly to explaining deviations in the experimentally-determined gyration radii of IDPs from the values expected based on the Flory scaling-law. By contrast, total proline content makes smaller contribution to explaining the effect of prolines on IDP conformation. Proline residues exhibit opposing effects depending on their organizational pattern in the IDP sequence. Clustered prolines (i.e., prolines with ≤2 intervening non-proline residues) result in expanded peptide conformations whereas isolated prolines (i.e., prolines with >2 intervening non-proline residues) impose compacted conformations. Clustered prolines were estimated to induce an expansion of ∼20% in IDP dimension (via formation of PPII structural elements) whereas isolated prolines were estimated to induce a compaction of ∼10% in IDP dimension (via the formation of backbone turns). This dual role of prolines provides a mechanism for conformational switching that does not rely on the kinetically much slower isomerization of cis proline to the trans form. Bioinformatic analysis demonstrates high populations of both isolated and clustered prolines and implementing them in coarse-grained molecular dynamics models illustrates that they improve the characterization of the conformational ensembles of IDPs.
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Affiliation(s)
- Milan Kumar Hazra
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Gilron
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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7
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Banavar JR, Giacometti A, Hoang TX, Maritan A, Škrbić T. A geometrical framework for thinking about proteins. Proteins 2023. [PMID: 37565735 DOI: 10.1002/prot.26567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise attraction that assembles these building blocks, while respecting their individual symmetries. Instead of seeking to mimic the complexity of proteins, we look for a simple abstraction of reality that yet captures the essence of proteins. We employ analytic calculations and detailed Monte Carlo simulations to explore some consequences of our theory. The predictions of our approach are in accord with experimental data. Our framework provides a rationalization for understanding the common characteristics of proteins. Our results show that the free energy landscape of a globular protein is pre-sculpted at the backbone level, sequences and functionalities evolve in the fixed backdrop of the folds determined by geometry and symmetry, and that protein structures are unique in being simultaneously characterized by stability, diversity, and sensitivity.
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Affiliation(s)
- Jayanth R Banavar
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon, USA
| | - Achille Giacometti
- Ca' Foscari University of Venice, Department of Molecular Sciences and Nanosystems, Venice, Italy
- European Centre for Living Technology (ECLT), Venice, Italy
| | - Trinh X Hoang
- Vietnam Academy of Science and Technology, Institute of Physics, Hanoi, Vietnam
| | - Amos Maritan
- University of Padua, Department of Physics and Astronomy, Padua, Italy
| | - Tatjana Škrbić
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon, USA
- Ca' Foscari University of Venice, Department of Molecular Sciences and Nanosystems, Venice, Italy
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8
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Phougat M, Sahni NS, Choudhury D. Multiway Analysis Reveals Hydrophobicity as the Sole Determinant of Dynamic Peptide-Acetonitrile-Water Association Behavior. J Phys Chem B 2023. [PMID: 37377430 DOI: 10.1021/acs.jpcb.3c02642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Multiway analysis, a class of techniques developed for the purpose of studying multi-dimensional multivariate data, has been applied to study the dynamical structure of the first solvation layer of Ace-Gly-X-Gly-Nme peptides (where X is any amino acid) perturbed with the increase in concentrations of acetonitrile. Separate MD simulations of each peptide were carried out in five different concentrations of acetonitrile. Association of peptide, water, and acetonitrile atoms was quantified in terms of the relative abundance of Delaunay tetrahedra whose vertices could be centered on either the peptide, acetonitrile, or water atoms. A three-way data set comprising nine types of Delaunay tetrahedra in the first dimension, five concentrations of acetonitrile in the second dimension, and 26 different peptides in the third dimension was subjected to two different multiway methods viz., the constrained PARAFAC and the unconstrained Tucker3 analysis. The results unequivocally show that the dynamic peptide-acetonitrile-water association behavior could be solely explained by the hydrophobicity of the central amino acid. The study also demonstrates the utility of multiway analysis for the integration and interpretation of large number of separate MD simulations.
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Affiliation(s)
- Monika Phougat
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Narinder Singh Sahni
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Devapriya Choudhury
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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9
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de Brevern AG. An agnostic analysis of the human AlphaFold2 proteome using local protein conformations. Biochimie 2023; 207:11-19. [PMID: 36417962 DOI: 10.1016/j.biochi.2022.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/14/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Knowledge of the 3D structure of proteins is a valuable asset for understanding their precise biological mechanisms. However, the cost of production of 3D structures and experimental difficulties limit their obtaining. The proposal of 3D structural models is consequently an appealing alternative. The release of the AlphaFold Deep Learning approach has revolutionized the field. The recent near-complete human proteome proposal makes it possible to analyse large amounts of data and evaluate the results of the approach in greater depth. The 3D human proteome was thus analysed in light of the classic secondary structures, and many less-used protein local conformations (PolyProline II helices, type of γ-turns, of β-turns and of β-bulges, curvature of the helices, and a structural alphabet). Without questioning the global quality of the approach, this analysis highlights certain local conformations, which maybe poorly predicted and they could therefore be better addressed.
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Affiliation(s)
- Alexandre G de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM UMR_S 1134, BIGR, DSIMB Bioinformatics team, F-75014, Paris, France.
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10
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Duan H, Li J, Xue J, Qi D. Metal-Enhanced Helical Chirality of Coil Macromolecules: Bioinspired by Metal Coordination-Induced Protein Folding. Biomacromolecules 2023; 24:344-357. [PMID: 36563170 DOI: 10.1021/acs.biomac.2c01165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although the supramolecular helical structures of biomacromolecules have been studied, the examples of supramolecular systems that are assembled using coils to form helical polymer chains are still limited. Inspired by enhanced helical chirality at the supramolecular level in metal coordination-induced protein folding, a series of alanine-based coil copolymers (poly-(l-co-d)-ala-NH2) carrying (l)- and (d)-alanine pendants were synthesized as a fresh research model to study the cooperative processes between homochirality property and metal coordination. The complexes of poly-(l-co-d)-ala-NH2 and metal ions underwent a coil-to-helix transition and exhibited remarkable nonlinear effects based on the enantiomeric excess of the monomer unit in the copolymers, affording enhanced helical chirality compared to poly-(l-co-d)-ala-NH2. More importantly, the synergistic effect of amplification of asymmetry and metal coordination triggered the formation of a helical molecular orbital on the polymer backbone via the coordination with the d orbital of copper ions. Thus, the helical chirality enhancement degree of poly-(l-co-d)-ala-NH2/Cu2+ complexes (31.4) is approximately 3 times higher than that of poly-(l-co-d)-ala-NH2/Ag+ complexes (9.8). This study not only provides important mechanistic insights into the enhancement of helical chirality for self-assembly but also establishes a new strategy for studying the homochiral amplification of asymmetry in biological supramolecular systems.
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Affiliation(s)
- Huimin Duan
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China.,Zhejiang Provincial Engineering Research Center for Green and Low-carbon Dyeing & Finishing, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Jiawei Li
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China.,Zhejiang Provincial Engineering Research Center for Green and Low-carbon Dyeing & Finishing, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China.,Zhejiang Provincial Innovation Center of Advanced Textile Technology, Shaoxing 312000, China
| | - Jiadan Xue
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Dongming Qi
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China.,Zhejiang Provincial Engineering Research Center for Green and Low-carbon Dyeing & Finishing, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China.,Zhejiang Provincial Innovation Center of Advanced Textile Technology, Shaoxing 312000, China
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11
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de Brevern AG. A Perspective on the (Rise and Fall of) Protein β-Turns. Int J Mol Sci 2022; 23:12314. [PMID: 36293166 PMCID: PMC9604201 DOI: 10.3390/ijms232012314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/21/2022] Open
Abstract
The β-turn is the third defined secondary structure after the α-helix and the β-sheet. The β-turns were described more than 50 years ago and account for more than 20% of protein residues. Nonetheless, they are often overlooked or even misunderstood. This poor knowledge of these local protein conformations is due to various factors, causes that I discuss here. For example, confusion still exists about the assignment of these local protein structures, their overlaps with other structures, the potential absence of a stabilizing hydrogen bond, the numerous types of β-turns and the software's difficulty in assigning or visualizing them. I also propose some ideas to potentially/partially remedy this and present why β-turns can still be helpful, even in the AlphaFold 2 era.
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Affiliation(s)
- Alexandre G de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM UMR_S 1134, BIGR, DSIMB Team, F-75014 Paris, France
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12
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Pak VV, Khojimatov OK, Pak AV, Sagdullaev SS, Yun L. Design of Tetrapeptides as a Competitive Inhibitor for HMG-CoA Reductase and Modeling Recognized Sequence as a β-Turn Structure. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10455-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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13
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Design, characterization and structure-function analysis of novel antimicrobial peptides based on the N-terminal CATH-2 fragment. Sci Rep 2022; 12:12058. [PMID: 35835842 PMCID: PMC9283491 DOI: 10.1038/s41598-022-16303-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/07/2022] [Indexed: 11/28/2022] Open
Abstract
The emergence of multidrug resistance coupled with shrinking antibiotic pipelines has increased the demand of antimicrobials with novel mechanisms of action. Therefore, researchers across the globe are striving to develop new antimicrobial substances to alleviate the pressure on conventional antibiotic therapies. Host-Defence Peptides (HDPs) and their derivatives are emerging as effective therapeutic agents against microbial resistance. In this study, five analogs (DP1-5) of the N-terminal (N-15) fragment of CATH-2 were designed based on the delicate balance between various physicochemical properties such as charge, aliphatic character, amphipathicity and hydrophobicity. By means of in-silico and in-vitro studies a novel peptide (DP1) with the sequence “RFGRFLRKILRFLKK” was found to be more effective and less toxic than the N-terminal CATH-2 peptide. Circular dichroism spectroscopy and differential scanning calorimetry were applied for structural insights. Antimicrobial, haemolytic, and cytotoxic activities were also assessed. The resulting peptide was characterized by low cytotoxicity, low haemolytic activity, and efficient anti-microbial activity. Structurally, it displayed strong helical properties irrespective of the solvent environment and was stable in membrane-mimicking environments. Taken together, the data suggests that DP1 can be explored as a promising therapeutic agent with possible clinical applications.
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14
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Shome M, Chung Y, Chavan R, Park JG, Qiu J, LaBaer J. Serum autoantibodyome reveals that healthy individuals share common autoantibodies. Cell Rep 2022; 39:110873. [PMID: 35649350 PMCID: PMC9221390 DOI: 10.1016/j.celrep.2022.110873] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/02/2022] [Accepted: 05/04/2022] [Indexed: 12/02/2022] Open
Abstract
Autoantibodies are a hallmark of both autoimmune disease and cancer, but
they also occur in healthy individuals. Here, we perform a meta-analysis of nine
datasets and focus on the common autoantibodies shared by healthy individuals.
We report 77 common autoantibodies based on the protein microarray data obtained
from probing 182 healthy individual sera on 7,653 human proteins and an
additional 90 healthy individual sera on 1,666 human proteins. There is no
gender bias; however, the number of autoantibodies increase with age, plateauing
around adolescence. We use a bioinformatics pipeline to determine possible
molecular-mimicry peptides that can contribute to the elicitation of these
common autoantibodies. There is enrichment of intrinsic properties of proteins
like hydrophilicity, basicity, aromaticity, and flexibility for common
autoantigens. Subcellular localization and tissue-expression analysis reveal
that several common autoantigens are sequestered from the circulating
autoantibodies. Shome et al. performed a meta-analysis to discover the common
autoantibodies found in healthy individuals. These common autoantibodies appear
and increase during youth and plateau at adolescence. Bioinformatics techniques
demonstrate the potential role of molecular mimicry in their production as well
as several common intrinsic biochemical properties.
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Affiliation(s)
- Mahasish Shome
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yunro Chung
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA; College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Ramani Chavan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jin G Park
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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15
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D'mello VC, Goldsztejn G, Rao Mundlapati V, Brenner V, Gloaguen E, Charnay‐Pouget F, Aitken DJ, Mons M. Characterization of Asx Turn Types and Their Connate Relationship with β‐Turns. Chemistry 2022; 28:e202104328. [DOI: 10.1002/chem.202104328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Viola C. D'mello
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Graphene Research Labs KIADB IT Park Near Airport Bengaluru 562149 India
| | - Gildas Goldsztejn
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Université Paris-Saclay, CNRS Institut des Sciences Moléculaires d'Orsay (ISMO) 91405 Orsay France
| | - Venkateswara Rao Mundlapati
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
- Present address: Institut de Recherche en Astrophysique et Planétologie (IRAP) Université de Toulouse (UPS), CNRS, CNES 9 Avenue du Colonel Roche 31028 Toulouse France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
| | - Florence Charnay‐Pouget
- Université Paris-Saclay, CNRS Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) 91405 Orsay France
- Present address: Université Clermont Auvergne, CNRS SIGMA Clermont, ICCF 63000 Clermont-Ferrand France
| | - David J. Aitken
- Université Paris-Saclay, CNRS Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) 91405 Orsay France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS Laboratoire Interactions Dynamiques et Lasers (LIDYL) 91191 Gif-sur-Yvette France
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16
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Becht DC, Leavens MJ, Zeng B, Rothfuss MT, Briknarová K, Bowler BE. Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A. Biochemistry 2022; 61:767-784. [PMID: 35430812 PMCID: PMC9150713 DOI: 10.1021/acs.biochem.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the first ubiquitin-associated domain from HHR23A, UBA(1), was determined by X-ray crystallography at a 1.60 Å resolution, and its stability, folding kinetics, and residual structure under denaturing conditions have been investigated. The concentration dependence of thermal denaturation and size-exclusion chromatography indicate that UBA(1) is monomeric. Guanidine hydrochloride (GdnHCl) denaturation experiments reveal that the unfolding free energy, ΔGu°'(H2O), of UBA(1) is 2.4 kcal mol-1. Stopped-flow folding kinetics indicates sub-millisecond folding with only proline isomerization phases detectable at 25 °C. The full folding kinetics are observable at 4 °C, yielding a folding rate constant, kf, in the absence of a denaturant of 13,000 s-1 and a Tanford β-value of 0.80, consistent with a compact transition state. Evaluation of the secondary structure via circular dichroism shows that the residual helical structure in the denatured state is replaced by polyproline II structure as the GdnHCl concentration increases. Analysis of NMR secondary chemical shifts for backbone 15NH, 13CO, and 13Cα atoms between 4 and 7 M GdnHCl shows three islands of residual helical secondary structure that align in sequence with the three native-state helices. Extrapolation of the NMR data to 0 M GdnHCl demonstrates that helical structure would populate to 17-33% in the denatured state under folding conditions. Comparison with NMR data for a peptide corresponding to helix 1 indicates that this helix is stabilized by transient tertiary interactions in the denatured state of UBA(1). The high helical content in the denatured state, which is enhanced by transient tertiary interactions, suggests a diffusion-collision folding mechanism.
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Affiliation(s)
- Dustin C. Becht
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Baisen Zeng
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Michael T. Rothfuss
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Klára Briknarová
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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17
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Singh MK, Lakshman MK. Recent developments in the utility of saturated azaheterocycles in peptidomimetics. Org Biomol Chem 2022; 20:963-979. [PMID: 35018952 DOI: 10.1039/d1ob01329g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To a large extent, the physical and chemical properties of peptidomimetic molecules are dictated by the integrated heterocyclic scaffolds they contain. Heterocyclic moieties are introduced into a majority of peptide-mimicking molecules to modulate conformational flexibility, improve bioavailability, and fine-tune electronics, and in order to achieve potency similar to or better than that of the natural peptide ligand. This mini-review delineates recent developments, limited to the past five years, in the utility of selected saturated 3- to 6-membered heterocyclic moieties in peptidomimetic design. Also discussed is the chemistry involved in the synthesis of the azaheterocyclic scaffolds and the structural implications of the introduction of these azaheterocycles in peptide backbones as well as side chains of the peptide mimics.
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Affiliation(s)
- Manish K Singh
- Department of Science, Technology, and Mathematics, Lincoln University, 820 Chestnut Street, Jefferson City, Missouri 65101, USA.
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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18
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Roy Chowdhury S, Haldar D. A gama-turn mimetic for selective sensing of Cu(II) and combinatorial multiple logic gate. CrystEngComm 2022. [DOI: 10.1039/d2ce00462c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have designed and synthesized a gama-turn mimetic using fenamic acid and α-aminoisobutyricacid (Aib), the conformation and optoelectronic properties of which can be changed by appropriate external stimuli. From single-crystal...
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19
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Sun XY, Zhong Y, Li YH, Miller DP, Buttan S, Wu XX, Zhang Y, Tang Q, Tan HW, Zhu J, Liu R, Zurek E, Lu ZL, Gong B. Reliable folding of hybrid tetrapeptides into short β-hairpins. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Neckebroeck A, Kelly SM, Smith BO, Clark JS. Synthesis of the Prototypical Cyclopropyl Dipeptide Mimic and Evaluation of Its Turn-Inducing Capability. J Org Chem 2021; 87:258-270. [PMID: 34913698 DOI: 10.1021/acs.joc.1c02344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The (+) and (-) enantiomers of a new turn-inducing cyclopropyl dipeptide mimic have been synthesized and evaluated. The mimic derives its turn-inducing capabilities solely from the cyclopropyl group and without the conformational biasing that would be provided by side-chain substituents. The mimic and peptide-mimic hybrids prepared from it have been studied using a combination of spectroscopic techniques (NMR, IR, and CD). The dipeptide mimic itself displays intramolecular hydrogen bonding in organic solvents, which differs from that observed in natural peptide turns. In contrast, more elaborate peptide-mimic hybrids exhibit hydrogen bonding characteristics that vary with solvent but are consistent with structures found in the tetrapeptide portion (i → i + 3) of a native β-turn.
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Affiliation(s)
- Albane Neckebroeck
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Sharon M Kelly
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Brian O Smith
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - J Stephen Clark
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, United Kingdom
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21
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Abstract
It has been a long-standing conviction that a protein's native fold is selected from a vast number of conformers by the optimal constellation of enthalpically favorable interactions. In marked contrast, this Perspective introduces a different mechanism, one that emphasizes conformational entropy as the principal organizer in protein folding while proposing that the conventional view is incomplete. This mechanism stems from the realization that hydrogen bond satisfaction is a thermodynamic necessity. In particular, a backbone hydrogen bond may add little to the stability of the native state, but a completely unsatisfied backbone hydrogen bond would be dramatically destabilizing, shifting the U(nfolded) ⇌ N(ative) equilibrium far to the left. If even a single backbone polar group is satisfied by solvent when unfolded but buried and unsatisfied when folded, that energy penalty alone, approximately +5 kcal/mol, would rival almost the entire free energy of protein stabilization, typically between -5 and -15 kcal/mol under physiological conditions. Consequently, upon folding, buried backbone polar groups must form hydrogen bonds, and they do so by assembling scaffolds of α-helices and/or strands of β-sheet, the only conformers in which, with rare exception, hydrogen bond donors and acceptors are exactly balanced. In addition, only a few thousand viable scaffold topologies are possible for a typical protein domain. This thermodynamic imperative winnows the folding population by culling conformers with unsatisfied hydrogen bonds, thereby reducing the entropy cost of folding. Importantly, conformational restrictions imposed by backbone···backbone hydrogen bonding in the scaffold are sequence-independent, enabling mutation─and thus evolution─without sacrificing the structure.
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Affiliation(s)
- George D Rose
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218-2683, United States
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22
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Sidorova A, Bystrov V, Lutsenko A, Shpigun D, Belova E, Likhachev I. Quantitative Assessment of Chirality of Protein Secondary Structures and Phenylalanine Peptide Nanotubes. NANOMATERIALS 2021; 11:nano11123299. [PMID: 34947648 PMCID: PMC8707344 DOI: 10.3390/nano11123299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 01/25/2023]
Abstract
In this study we consider the features of spatial-structure formation in proteins and their application in bioengineering. Methods for the quantitative assessment of the chirality of regular helical and irregular structures of proteins are presented. The features of self-assembly of phenylalanine (F) into peptide nanotubes (PNT), which form helices of different chirality, are also analyzed. A method is proposed for calculating the magnitude and sign of the chirality of helix-like peptide nanotubes using a sequence of vectors for the dipole moments of individual peptides.
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Affiliation(s)
- Alla Sidorova
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.L.); (D.S.); (E.B.)
- Correspondence:
| | - Vladimir Bystrov
- Institute of Mathematical Problems of Biology, The Branch of Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Russia; (V.B.); (I.L.)
| | - Aleksey Lutsenko
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.L.); (D.S.); (E.B.)
| | - Denis Shpigun
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.L.); (D.S.); (E.B.)
| | - Ekaterina Belova
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.L.); (D.S.); (E.B.)
| | - Ilya Likhachev
- Institute of Mathematical Problems of Biology, The Branch of Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Russia; (V.B.); (I.L.)
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23
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Prediction of suitable T and B cell epitopes for eliciting immunogenic response against SARS-CoV-2 and its mutant. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS 2021; 11:1. [PMID: 34849327 PMCID: PMC8619655 DOI: 10.1007/s13721-021-00348-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/21/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022]
Abstract
Spike glycoprotein of SARS-CoV-2 is mainly responsible for the recognition and membrane fusion within the host and this protein has an ability to mutate. Hence, T cell and B cell epitopes were derived from the spike glycoprotein sequence of wild SARS-CoV-2. The proposed T cell and B cell epitopes were found to be antigenic and conserved in the sequence of SARS-CoV-2 mutant (B.1.1.7). Thus, the proposed epitopes are effective against SARS-CoV-2 and its B.1.1.7 mutant. MHC-I that best interacts with the proposed T cell epitopes were found, using immune epitope database. Molecular docking and molecular dynamic simulations were done for ensuring a good binding between the proposed MHC-I and T cell epitopes. The finally proposed T cell epitope was found to be antigenic, non-allergenic, non-toxic and stable. Further, the finally proposed B cell epitopes were also found to be antigenic. The population conservation analysis has ensured the presence of MHC-I molecule (respective to the finally proposed T cell) in human population of most affected countries with SARS-CoV-2. Thus the proposed T and B cell epitope could be effective in designing an epitope-based vaccine, which is effective on SARS-CoV-2 and its B.1.1.7mutant. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13721-021-00348-w.
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24
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Stanojlovic V, Müller A, Moazzam A, Hinterholzer A, Ożga K, Berlicki Ł, Schubert M, Cabrele C. A Conformationally Stable Acyclic β-Hairpin Scaffold Tolerating the Incorporation of Poorly β-Sheet-Prone Amino Acids. Chembiochem 2021; 23:e202100604. [PMID: 34856053 PMCID: PMC9299858 DOI: 10.1002/cbic.202100604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Indexed: 11/09/2022]
Abstract
The β-hairpin is a structural element of native proteins, but it is also a useful artificial scaffold for finding lead compounds to convert into peptidomimetics or non-peptide structures for drug discovery. Since linear peptides are synthetically more easily accessible than cyclic ones, but are structurally less well-defined, we propose XWXWXpPXK(/R)X(R) as an acyclic but still rigid β-hairpin scaffold that is robust enough to accommodate different types of side chains, regardless of the secondary-structure propensity of the X residues. The high conformational stability of the scaffold results from tight contacts between cross-strand cationic and aromatic side chains, combined with the strong tendency of the d-Pro-l-Pro dipeptide to induce a type II' β-turn. To demonstrate the robustness of the scaffold, we elucidated the NMR structures and performed molecular dynamics (MD) simulations of a series of peptides displaying mainly non-β-branched, poorly β-sheet-prone residues at the X positions. Both the NMR and MD data confirm that our acyclic β-hairpin scaffold is highly versatile as regards the amino-acid composition of the β-sheet face opposite to the cationic-aromatic one.
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Affiliation(s)
- Vesna Stanojlovic
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Anna Müller
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Ali Moazzam
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.,School of Chemistry, College of Science, University of Tehran, P.O. Box 14155-6619, Tehran, Iran
| | - Arthur Hinterholzer
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
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25
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Mundlapati VR, Imani Z, D'mello VC, Brenner V, Gloaguen E, Baltaze JP, Robin S, Mons M, Aitken DJ. N-H⋯X interactions stabilize intra-residue C5 hydrogen bonded conformations in heterocyclic α-amino acid derivatives. Chem Sci 2021; 12:14826-14832. [PMID: 34820098 PMCID: PMC8597926 DOI: 10.1039/d1sc05014a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Nature makes extensive and elaborate use of hydrogen bonding to assemble and stabilize biomolecular structures. The shapes of peptides and proteins rely significantly on N–H⋯O
Created by potrace 1.16, written by Peter Selinger 2001-2019
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C interactions, which are the linchpins of turns, sheets and helices. The C5 H-bond, in which a single residue provides both donor and acceptor, is generally considered too weak to force the backbone to adopt extended structures. Exploiting the synergy between gas phase (experimental and quantum chemistry) and solution spectroscopies to decipher IR spectroscopic data, this work demonstrates that the extended C5-based conformation in 4-membered ring heterocyclic α-amino acid derivatives is significantly stabilized by the formation of an N–H⋯X H-bond. In this synergic system the strength of the C5 interaction remains constant while the N–H⋯X H-bond strength, and thereby the support provided by it, varies with the heteroatom. In 4-membered ring heterocyclic α-amino acid derivatives, extended conformations based on intraresidue C5 H-bonds can be stabilized by N–H⋯X H-bonds, making the combined C5–C6γ structures prominent in both gas phase and in weakly polar solutions.![]()
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Affiliation(s)
| | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France
| | - Viola C D'mello
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | | | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France .,Université de Paris, Faculté de Pharmacie 75006 Paris France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
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26
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Paiz EA, Allen JH, Correia JJ, Fitzkee NC, Hough LE, Whitten ST. Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins. J Biol Chem 2021; 297:101343. [PMID: 34710373 PMCID: PMC8592878 DOI: 10.1016/j.jbc.2021.101343] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
The complex cellular milieu can spontaneously demix, or phase separate, in a process controlled in part by intrinsically disordered (ID) proteins. A protein's propensity to phase separate is thought to be driven by a preference for protein-protein over protein-solvent interactions. The hydrodynamic size of monomeric proteins, as quantified by the polymer scaling exponent (v), is driven by a similar balance. We hypothesized that mean v, as predicted by protein sequence, would be smaller for proteins with a strong propensity to phase separate. To test this hypothesis, we analyzed protein databases containing subsets of proteins that are folded, disordered, or disordered and known to spontaneously phase separate. We find that the phase-separating disordered proteins, on average, had lower calculated values of v compared with their non-phase-separating counterparts. Moreover, these proteins had a higher sequence-predicted propensity for β-turns. Using a simple, surface area-based model, we propose a physical mechanism for this difference: transient β-turn structures reduce the desolvation penalty of forming a protein-rich phase and increase exposure of atoms involved in π/sp2 valence electron interactions. By this mechanism, β-turns could act as energetically favored nucleation points, which may explain the increased propensity for turns in ID regions (IDRs) utilized biologically for phase separation. Phase-separating IDRs, non-phase-separating IDRs, and folded regions could be distinguished by combining v and β-turn propensity. Finally, we propose a new algorithm, ParSe (partition sequence), for predicting phase-separating protein regions, and which is able to accurately identify folded, disordered, and phase-separating protein regions based on the primary sequence.
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Affiliation(s)
- Elisia A Paiz
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Jeffre H Allen
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - John J Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Loren E Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA.
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA.
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27
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Škrbić T, Maritan A, Giacometti A, Rose GD, Banavar JR. Building blocks of protein structures: Physics meets biology. Phys Rev E 2021; 104:014402. [PMID: 34412233 DOI: 10.1103/physreve.104.014402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022]
Abstract
The native state structures of globular proteins are stable and well packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry of the building blocks of protein structures-α helices and strands assembled into β sheets-with no adjustable parameters, no amino acid sequence information, and no chemistry. There is an almost perfect fit between the dictates of mathematics and physics and the rules of quantum chemistry. Protein evolution is facilitated by sequence-independent platforms, which can elaborate sequence-dependent functional diversity. Our work highlights the vital role of discreteness in life and may have implications for the creation of artificial life and on the nature of life elsewhere in the cosmos.
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Affiliation(s)
- Tatjana Škrbić
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA.,Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
| | - Amos Maritan
- Dipartimento di Fisica e Astronomia, Università di Padova and INFN, via Marzolo 8, 35131 Padova, Italy
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.,European Center for Living Technologies (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venezia, Italy
| | - George D Rose
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218-2683, USA
| | - Jayanth R Banavar
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA
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Catalini S, Rossi B, Tortora M, Foggi P, Gessini A, Masciovecchio C, Bruni F. Hydrogen Bonding and Solvation of a Proline-Based Peptide Model in Salt Solutions. Life (Basel) 2021; 11:life11080824. [PMID: 34440568 PMCID: PMC8400059 DOI: 10.3390/life11080824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
The hydrogen bonding of water and water/salt mixtures around the proline-based tripeptide model glycyl-l-prolyl-glycinamide·HCl (GPG-NH2) is investigated here by multi-wavelength UV resonance Raman spectroscopy (UVRR) to clarify the role of ion–peptide interactions in affecting the conformational stability of this peptide. The unique sensitivity and selectivity of the UVRR technique allow us to efficiently probe the hydrogen bond interaction between water molecules and proline residues in different solvation conditions, along with its influence on trans to cis isomerism in the hydrated tripeptide. The spectroscopic data suggest a relevant role played by the cations in altering the solvation shell at the carbonyl site of proline., while the fluoride and chloride anions were found to promote the establishment of the strongest interactions on the C=O site of proline. This latter effect is reflected in the greater stabilization of the trans conformers of the tripeptide in the presence of these specific ions. The molecular view provided by UVRR experiments was complemented by the results of circular dichroism (CD) measurements that show a strong structural stabilizing effect on the β-turn motif of GPG-NH2 observed in the presence of KF as a co-solute.
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Affiliation(s)
- Sara Catalini
- European Laboratory for Non-Linear Spectroscopy, LENS, Via Nello Carrara, 1, 50019 Sesto Fiorentino, Italy; (S.C.); (P.F.)
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
- Correspondence:
| | - Mariagrazia Tortora
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
- Area Science Park, Padriciano, 99, 34149 Trieste, Italy
| | - Paolo Foggi
- European Laboratory for Non-Linear Spectroscopy, LENS, Via Nello Carrara, 1, 50019 Sesto Fiorentino, Italy; (S.C.); (P.F.)
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; (M.T.); (A.G.); (C.M.)
| | - Fabio Bruni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale, 84, 00146 Roma, Italy;
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29
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Springfield E, Willis A, Merle J, Mazlo J, Ngu-Schwemlein M. Spectroscopic and Theoretical Studies of Hg(II) Complexation with Some Dicysteinyl Tetrapeptides. Bioinorg Chem Appl 2021; 2021:9911474. [PMID: 34349795 PMCID: PMC8328728 DOI: 10.1155/2021/9911474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/10/2021] [Indexed: 11/17/2022] Open
Abstract
Tetrapeptides containing a Cys-Gly-Cys motif and a propensity to adopt a reverse-turn structure were synthesized to evaluate how O-, N-, H-, and aromatic π donor groups might contribute to mercury(II) complex formation. Tetrapeptides Xaa-Cys-Gly-Cys, where Xaa is glycine, glutamate, histidine, or tryptophan, were prepared and reacted with mercury(II) chloride. Their complexation with mercury(II) was studied by spectroscopic methods and computational modeling. UV-vis studies confirmed that mercury(II) binds to the cysteinyl thiolates as indicated by characteristic ligand-to-metal-charge-transfer transitions for bisthiolated S-Hg-S complexes, which correspond to 1 : 1 mercury-peptide complex formation. ESI-MS data also showed dominant 1 : 1 mercury-peptide adducts that are consistent with double deprotonations from the cysteinyl thiols to form thiolates. These complexes exhibited a strong positive circular dichroism band at 210 nm and a negative band at 193 nm, indicating that these peptides adopted a β-turn structure after binding mercury(II). Theoretical studies confirmed that optimized 1 : 1 mercury-peptide complexes adopt β-turns stabilized by intramolecular hydrogen bonds. These optimized structures also illustrate how specific N-terminal side-chain donor groups can assume intramolecular interactions and contribute to complex stability. Fluorescence quenching results provided supporting data that the indole donor group could interact with the coordinated mercury. The results from this study indicate that N-terminal side-chain residues containing carboxylate, imidazole, or indole groups can participate in stabilizing dithiolated mercury(II) complexes. These structural insights on peripheral mercury-peptide interactions provide additional understanding of the chemistry of mercury(II) with side-chain donor groups in peptides.
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Affiliation(s)
- Elliot Springfield
- Chemistry Department, Winston Salem State University, Winston-Salem, NC 27110, USA
| | - Alana Willis
- Chemistry Department, Winston Salem State University, Winston-Salem, NC 27110, USA
| | - John Merle
- Chemistry Department, Winston Salem State University, Winston-Salem, NC 27110, USA
| | - Johanna Mazlo
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Maria Ngu-Schwemlein
- Chemistry Department, Winston Salem State University, Winston-Salem, NC 27110, USA
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30
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Dongre AV, Das S, Bellur A, Kumar S, Chandrashekarmath A, Karmakar T, Balaram P, Balasubramanian S, Balaram H. Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation. Biophys J 2021; 120:3732-3746. [PMID: 34302792 DOI: 10.1016/j.bpj.2021.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/18/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022] Open
Abstract
Stability of proteins from hyperthermophiles (organisms existing under boiling water conditions) enabled by a reduction of conformational flexibility is realized through various mechanisms. A succinimide (SNN) arising from the post-translational cyclization of the side chains of aspartyl/asparaginyl residues with the backbone amide -NH of the succeeding residue would restrain the torsion angle Ψ and can serve as a new route for hyperthermostability. However, such a succinimide is typically prone to hydrolysis, transforming to either an aspartyl or β-isoaspartyl residue. Here, we present the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase and, using enhanced sampling molecular dynamics simulations, address the mechanism of its increased thermostability, up to 100°C, imparted by an unexpectedly stable succinimidyl residue at position 109. The stability of SNN109 to hydrolysis is seen to arise from its electrostatic shielding by the side-chain carboxylate group of its succeeding residue Asp110, as well as through n → π∗ interactions between SNN109 and its preceding residue Glu108, both of which prevent water access to SNN. The stable succinimidyl residue induces the formation of an α-turn structure involving 13-atom hydrogen bonding, which locks the local conformation, reducing protein flexibility. The destabilization of the protein upon replacement of SNN with a Φ-restricted prolyl residue highlights the specificity of the succinimidyl residue in imparting hyperthermostability to the enzyme. The conservation of the succinimide-forming tripeptide sequence (E(N/D)(E/D)) in several archaeal GATases strongly suggests an adaptation of this otherwise detrimental post-translational modification as a harbinger of thermostability.
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Affiliation(s)
- Aparna Vilas Dongre
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Sudip Das
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Asutosh Bellur
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Anusha Chandrashekarmath
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Tarak Karmakar
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India; Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano, Ticino, Switzerland; Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Lugano, Ticino, Switzerland
| | - Padmanabhan Balaram
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India.
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India.
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31
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Naveed M, Tehreem S, Arshad S, Bukhari SA, Shabbir MA, Essa R, Ali N, Zaib S, Khan A, Al-Harrasi A, Khan I. Design of a novel multiple epitope-based vaccine: An immunoinformatics approach to combat SARS-CoV-2 strains. J Infect Public Health 2021; 14:938-946. [PMID: 34119848 PMCID: PMC8093003 DOI: 10.1016/j.jiph.2021.04.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Since the SARS-CoV-2 outbreak in December 2019 in Wuhan, China, the virus has infected more than 153 million individuals across the world due to its human-to-human transmission. The USA is the most affected country having more than 32-million cases till date. Sudden high fever, pneumonia and organ failure have been observed in infected individuals. OBJECTIVES In the current situation of emerging viral disease, there is no specific vaccine, or any therapeutics available for SARS-CoV-2, thus there is a dire need to design a potential vaccine to combat the virus by developing immunity in the population. The purpose of present study was to develop a potential vaccine by targeting B and T-cell epitopes using bioinformatics approaches. METHODS B- and T-cell epitopes are predicted from novel M protein-SARS-CoV-2 for the development of a unique multiple epitope vaccine by applying bioinformatics approaches. These epitopes were analyzed and selected for their immunogenicity, antigenicity scores, and toxicity in correspondence to their ability to trigger immune response. In combination to epitopes, best multi-epitope of potential immunogenic property was constructed. The epitopes were joined using EAAAK, AAY and GPGPG linkers. RESULTS The constructed vaccine showed good results of worldwide population coverage and promising immune response. This constructed vaccine was subjected to in-silico immune simulations by C-ImmSim. Chimeric protein construct was cloned into PET28a (+) vector for expression study in Escherichia coli using snapgene. CONCLUSION This vaccine design proved effective in various computer-based immune response analysis as well as showed good population coverage. This study is solely dependent on developing M protein-based vaccine, and these in silico findings would be a breakthrough in the development of an effective vaccine to eradicate SARS-CoV-2 globally.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan.
| | - Sana Tehreem
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Sundas Arshad
- Faculty of Science, Technology and Medicine, University of Luxembourg, Luxembourg
| | - Syeda Aniqa Bukhari
- Research Center for Modeling and Simulation, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Ramsha Essa
- Center of Excellence in Molecular Biology (CEMB), Punjab University, Lahore, Pakistan
| | - Nouman Ali
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Sumera Zaib
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, P.O Box 33, Postal Code 616, Birkat Al Mauz, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, P.O Box 33, Postal Code 616, Birkat Al Mauz, Nizwa, Oman.
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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32
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Zhang X, Ligny R, Chewchanwuttiwong S, Hadade R, Laurent MY, Martel A, Jacquemmoz C, Lhoste J, Bricaud S, Py S, Dujardin G. δ-Valerolactamic Quaternary Amino Acid Derivatives: Enantiodivergent Synthesis and Evidence for Stereodifferentiated β-Turn-Inducing Properties. J Org Chem 2021; 86:8041-8055. [PMID: 33960779 DOI: 10.1021/acs.joc.1c00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Enantiopure (R) and (S) cyclic α,α-disubstituted amino acid derivatives displaying a δ-valerolactam side chain were prepared from a common isoxazolidine precursor. The (R)-configured δ-valerolactam 11 was converted into diastereoisomeric pseudopeptides to investigate its ability to induce secondary structures in peptidomimetics. Conformational studies of these pseudopeptides were carried out in the solid state (X-ray diffraction), in solution (NMR analyses), and in silico (computer-aided conformational analysis), which demonstrated that such quaternary amino acids induce β-turn conformations stable enough to be retained in polar media (DMSO). Incorporation of this new type of α,α-disubstituted amino acid into a representative pseudopeptidic sequence by N- then C-elongation and N-debenzylation is also described herein and could serve for the synthesis of various structured peptidomimetics.
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Affiliation(s)
- Xiaofei Zhang
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France.,Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France.,CNRS, DCM, F-38000 Grenoble, France
| | - Romain Ligny
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Sopa Chewchanwuttiwong
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France.,Prince of Songkla University, Faculty of Science and Industrial Technology Surat Thani 84000, Thailand
| | - Rawan Hadade
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Mathieu Y Laurent
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Arnaud Martel
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Corentin Jacquemmoz
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Jérôme Lhoste
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Sullivan Bricaud
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Sandrine Py
- Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France.,CNRS, DCM, F-38000 Grenoble, France
| | - Gilles Dujardin
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
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33
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Goyal R, Jerath G, Akhil R, Chandrasekharan A, Puppala ER, Ponneganti S, Sarma A, Naidu VGM, Santhoshkumar TR, Ramakrishnan V. Geometry encoded functional programming of tumor homing peptides for targeted drug delivery. J Control Release 2021; 333:16-27. [PMID: 33722612 DOI: 10.1016/j.jconrel.2021.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/24/2021] [Accepted: 03/07/2021] [Indexed: 01/10/2023]
Abstract
Poly-peptide molecules have shown promising applications in drug delivery and tumor targeting. A series of tumor homing peptides were designed by exhaustively sampling low energy geometrical basins of amino acids at specific sites of a peptide molecule to induce a conformational lock. This peptide library was pruned to a limited set of eight molecules, employing electrostatic interactions, docking, and molecular dynamics simulations. These designed and optimized peptides were synthesized and tested on various cell lines, including breast cancer (MDA-MB-231), cervical cancer (HeLa), osteosarcoma (U2-OS), and non-cancerous mammary epithelial cells (MCF-10A) using confocal microscopy and flow cytometry. Peptides show differential uptake in cancerous MDA-MB-231, HeLa, U2-OS, and non-cancerous MCF-10A cells. Confocal imaging verified their ability to penetrate even in 3D tumorospheres of MDA-MB-231 cells. Further, experiments of mitochondrial membrane potential depolarization and Caspase-3 activation confirmed that their cytotoxic effects are by apoptosis. Homing ability of the designed peptides in in vivo system and fluorescence imaging with clinical samples of human origin have further confirmed that the in vitro studies are qualitatively identical and quantitatively comparable in their ability to selectively recognize tumor cells. Overall, we present a roadmap for the functional programming of peptide-based homing and penetrating molecules that can perform selective tumor targeting.
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Affiliation(s)
- Ruchika Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Gaurav Jerath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - R Akhil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Aneesh Chandrasekharan
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India
| | - Eswara Rao Puppala
- National Institute of Pharmaceutical Education and Research Guwahati, Guwahati 781101, Assam, India
| | - Srikanth Ponneganti
- National Institute of Pharmaceutical Education and Research Guwahati, Guwahati 781101, Assam, India
| | - Anupam Sarma
- Dr. Bhubaneswar Borooah Cancer Institute, Tata Memorial Centre (Mumbai), Guwahati 781016, Assam, India
| | - V G M Naidu
- National Institute of Pharmaceutical Education and Research Guwahati, Guwahati 781101, Assam, India
| | - T R Santhoshkumar
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India.
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Škrbić T, Maritan A, Giacometti A, Banavar JR. Local sequence-structure relationships in proteins. Protein Sci 2021; 30:818-829. [PMID: 33511717 PMCID: PMC7980514 DOI: 10.1002/pro.4032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/11/2022]
Abstract
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the putative native state folds from myriad possible conformations? In order to address these questions, we represent the local structure of each Cα atom of a protein by just two angles, θ and μ, and we analyze a set of more than 4,000 protein structures from the PDB. We use a hierarchical clustering scheme to divide the 20 amino acids into six distinct groups based on their similarity to each other in fitting local structural space. We present the results of a detailed analysis of patterns of amino acid specificity in adopting local structural conformations and show that the sequence-structure correlation is not very strong compared with a random assignment of sequence to structure. Yet, our analysis may be useful to determine an effective scoring rubric for quantifying the match of an amino acid to its putative local structure.
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Affiliation(s)
- Tatjana Škrbić
- Department of Physics and Institute for Fundamental ScienceUniversity of OregonEugeneOregonUSA
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari VeneziaVenezia MestreItaly
| | - Amos Maritan
- Dipartimento di Fisica e AstronomiaUniversità di Padova and INFNPadovaItaly
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari VeneziaVenezia MestreItaly
| | - Jayanth R. Banavar
- Department of Physics and Institute for Fundamental ScienceUniversity of OregonEugeneOregonUSA
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35
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Lameiras P, Nuzillard JM. Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 123:1-50. [PMID: 34078536 DOI: 10.1016/j.pnmrs.2020.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/06/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between 1H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).
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Affiliation(s)
- Pedro Lameiras
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
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36
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Parajuli P, Sable R, Shrestha L, Dahal A, Gauthier T, Taneja V, Jois S. Modulation of co-stimulatory signal from CD2-CD58 proteins by a grafted peptide. Chem Biol Drug Des 2021; 97:607-627. [PMID: 32946175 PMCID: PMC8717467 DOI: 10.1111/cbdd.13797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 06/23/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Peptides were designed to inhibit the protein-protein interaction of CD2 and CD58 to modulate the immune response. This work involved the design and synthesis of eight different peptides by replacing each amino acid residue in peptide 6 with alanine as well as grafting the peptide to the sunflower trypsin-inhibitor framework. From the alanine scanning studies, mutation at position 2 of the peptide was shown to result in increased potency to inhibit cell adhesion interactions. The most potent peptide from the alanine scanning was further studied for its detailed three-dimensional structure and binding to CD58 protein using surface plasmon resonance and flow cytometry. This peptide was used to graft to the sunflower trypsin inhibitor to improve the stability of the peptide. The grafted peptide, SFTI-a1, was further studied for its potency as well as its thermal, chemical, and enzymatic stability. The grafted peptide exhibited improved activity compared to our previously grafted peptide and was stable against thermal and enzymatic degradation.
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Affiliation(s)
- Pravin Parajuli
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
| | - Rushikesh Sable
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
| | - Leeza Shrestha
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
| | - Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
| | - Ted Gauthier
- Biotechnology Laboratory, LSU AgCenter, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Seetharama Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
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37
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Chu B, He JM, Liu LL, Wu CX, You LL, Li XL, Wang S, Chen CS, Tu M. Proangiogenic Peptide Nanofiber Hydrogels for Wound Healing. ACS Biomater Sci Eng 2021; 7:1100-1110. [PMID: 33512985 DOI: 10.1021/acsbiomaterials.0c01264] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rapid vascularization is vital for dermal regeneration, nutrient and nutrition transfer, metabolic waste removal, and prevention of infection. This study reports on a series of proangiogenic peptides designed to undergo self-assembly and promote angiogenesis and hence skin regeneration. The proangiogenic peptides comprised an angiogenic peptide segment, GEETEVTVEGLEPG, and a β-sheet structural peptide sequence. These peptides dissolved easily in ultrapure water and rapidly self-assembled into hydrogels in a pH-dependent manner, creating three-dimensional fibril network structures and nanofibers as revealed by a scanning microscope and a transmission electron microscope. In vitro experiments showed that the peptide hydrogels favored adhesion and proliferation of mouse fibroblasts (L929) and human umbilical vein endothelial cells (HUVECs). In particular, many connected tubes were formed in the HUVECs after 8 h of culture on the peptide hydrogels. In vivo experiments demonstrated that new blood vessels grew into the proangiogenic peptide hydrogels within 2 weeks after subcutaneous implantation in mice. Moreover, the proangiogenic-combined hydrogels exhibited faster repair cycles and better healing of skin defects. Collectively, the results indicate that the proangiogenic peptide hydrogels are a promising therapeutic option for skin regeneration.
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Affiliation(s)
- Bin Chu
- Department of Biomedical Engineering, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, P. R. China.,Key Laboratory of Biomedical Materials and Implant Devices, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057, P. R. China
| | - Jin-Mei He
- Key Laboratory of Biomedical Materials and Implant Devices, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057, P. R. China
| | - Lan-Lan Liu
- Key Laboratory of Biomedical Materials and Implant Devices, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057, P. R. China
| | - Chao-Xi Wu
- Department of Biomedical Engineering, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, P. R. China
| | - Ling-Ling You
- Department of Biomedical Engineering, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, P. R. China
| | - Xiao-Li Li
- Key Laboratory of Biomedical Materials and Implant Devices, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057, P. R. China
| | - Song Wang
- Key Laboratory of Biomedical Materials and Implant Devices, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057, P. R. China
| | - Chang-Sheng Chen
- Key Laboratory of Biomedical Materials and Implant Devices, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057, P. R. China
| | - Mei Tu
- Department of Biomedical Engineering, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, P. R. China
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38
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Leusciatti M, Mannucci B, Recca T, Quadrelli P. Turn-folding in fluorescent anthracene-substituted cyclopenta[ d]isoxazoline short peptides. RSC Adv 2021; 11:19551-19559. [PMID: 35479239 PMCID: PMC9033613 DOI: 10.1039/d1ra03685h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 11/28/2022] Open
Abstract
Cyclopenta[d]isoxazoline aminols were used for the synthesis of β-turn mimics. The peptide chain choice ascertained the influence of their structural features on the applicability/reliability/robustness of these scaffolds as β-turn inducers and their limitations. The amino acid selection as well as steric demands can favor or disfavor the structure folding and the correct design of the peptide chains deeply influences the potential use of these nitrosocarbonyl-based compounds as turn-inducers. Cyclopenta[d]isoxazoline aminols were used for the synthesis of β-turn mimics.![]()
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Affiliation(s)
| | - Barbara Mannucci
- Centro Grandi Strumenti (CGS)
- University of Pavia
- 27100 – Pavia
- Italy
| | - Teresa Recca
- Centro Grandi Strumenti (CGS)
- University of Pavia
- 27100 – Pavia
- Italy
| | - Paolo Quadrelli
- Department of Chemistry
- University of Pavia
- 27100 – Pavia
- Italy
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39
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Song Y, Schaufelberger F, Ashbridge Z, Pirvu L, Vitorica-Yrezabal IJ, Leigh DA. Effects of turn-structure on folding and entanglement in artificial molecular overhand knots. Chem Sci 2020; 12:1826-1833. [PMID: 34163946 PMCID: PMC8179330 DOI: 10.1039/d0sc05897a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The length and constitution of spacers linking three 2,6-pyridinedicarboxamide units in a molecular strand influence the tightness of the resulting overhand (open-trefoil) knot that the strand folds into in the presence of lanthanide(iii) ions. The use of β-hairpin forming motifs as linkers enables a metal-coordinated pseudopeptide with a knotted tertiary structure to be generated. The resulting pseudopeptide knot has one of the highest backbone-to-crossing ratios (BCR)—a measure of knot tightness (a high value corresponding to looseness)—for a synthetic molecular knot to date. Preorganization in the crossing-free turn section of the knot affects aromatic stacking interactions close to the crossing region. The metal-coordinated pseudopeptide knot is compared to overhand knots with other linkers of varying tightness and turn preorganization, and the entangled architectures characterized by NMR spectroscopy, ESI-MS, CD spectroscopy and, in one case, X-ray crystallography. The results show how it is possible to program specific conformational properties into different key regions of synthetic molecular knots, opening the way to systems where knotting can be systematically incorporated into peptide-like chains through design. Spacers linking 2,6-pyridinedicarboxamide units influence the tightness of the corresponding lanthanide-coordinated overhand knot. β-Hairpin forming motifs generate a metal-coordinated pseudopeptide with a knotted tertiary structure.![]()
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Affiliation(s)
- Yiwei Song
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China
| | | | - Zoe Ashbridge
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Lucian Pirvu
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | | | - David A Leigh
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China .,Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
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40
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Jyotisha, Singh S, Qureshi IA. Multi-epitope vaccine against SARS-CoV-2 applying immunoinformatics and molecular dynamics simulation approaches. J Biomol Struct Dyn 2020; 40:2917-2933. [PMID: 33164664 PMCID: PMC7682209 DOI: 10.1080/07391102.2020.1844060] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
COVID-19, caused by SARS-CoV-2, is severe respiratory illnesses leading to millions of deaths worldwide in very short span. The high case fatality rate and the lack of medical counter measures emphasize for an urgent quest to develop safe and effective vaccine. Receptor-binding domain (RBD) of spike protein of SARS-CoV-2 binds to the ACE2 receptor on human host cell for the viral attachment and entry, hence considered as a key target to develop vaccines, antibodies and therapeutics. In this study, immunoinformatics approach was employed to design a novel multi-epitope vaccine using RBD of SARS-CoV-2 spike protein. The potential B- and T-cell epitopes were selected from RBD sequence using various bioinformatics tools to design the vaccine construct. The in silico designed multi-epitope vaccine encompasses 146 amino acids with an adjuvant (human beta-defensin-2), which was further computationally evaluated for several parameters including antigenicity, allergenicity and stability. Subsequently, three-dimensional structure of vaccine construct was modelled and then docked with various toll-like receptors. Molecular dynamics (MD) study of docked TLR3-vaccine complex delineated it to be highly stable during simulation time and the stabilization of interaction was majorly contributed by electrostatic energy. The docked complex also showed low deformation and increased rigidity in motion of residues during dynamics. Furthermore, in silico cloning of the multi-epitope vaccine was carried out to generate the plasmid construct for expression in a bacterial system. Altogether, our study suggests that the designed vaccine candidate containing RBD region could provide the specific humoral and cell-mediated immune responses against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Jyotisha
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Samayaditya Singh
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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41
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Madhanagopal BR, Kumar J, Ganesh KN. Silver assisted stereo-directed assembly of branched peptide nucleic acids into four-point nanostars. NANOSCALE 2020; 12:21665-21673. [PMID: 33094774 DOI: 10.1039/d0nr05471b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Branched chiral peptide nucleic acids br(4S/R)-PNA with three arms of PNA-C4 strands were constructed on a central chiral core of 4(R/S)-aminoproline as the branching center. The addition of Ag+ triggered the self-assembly of branched PNAs through the formation of C-Ag+-C metallo base pairing of the three PNA C4 arms leading to non-covalent dendrimers, whose architecture is directed by the C4(R/S)-stereocenter of core 4-aminoproline. The 4S-aminoprolyl core enabled the precise formation of four-pointed nanostars that was not realised with 4R-aminoprolyl or acyclic, achiral aminoethyl glycyl PNA cores. The dendritic assembly of 4 pointed nanostars exhibited net chirality of base stacks in CD spectra, while the base stack assembly from br(4R)-PNA 2 was overall achiral. The results demonstrate that the silver assisted, 4S-aminoproline core stereo selective chiral assembly of branched PNAs manifests into nanostar morphology. The chiral branched PNAs open new vistas in the supramolecular organization of nucleic acids.
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Affiliation(s)
- Bharath Raj Madhanagopal
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India.
| | - Jatish Kumar
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India.
| | - Krishna N Ganesh
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India. and Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, Maharashtra, India
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42
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Imani Z, Mundlapati VR, Goldsztejn G, Brenner V, Gloaguen E, Guillot R, Baltaze JP, Le Barbu-Debus K, Robin S, Zehnacker A, Mons M, Aitken DJ. Conformation control through concurrent N-H⋯S and N-H⋯O[double bond, length as m-dash]C hydrogen bonding and hyperconjugation effects. Chem Sci 2020; 11:9191-9197. [PMID: 34123167 PMCID: PMC8163419 DOI: 10.1039/d0sc03339a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In addition to the classical N-H⋯O[double bond, length as m-dash]C non-covalent interaction, less conventional types of hydrogen bonding, such as N-H⋯S, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane α-amino acid. 6-Membered ring inter-residue N-H⋯S interactions (C6γ), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N-H⋯O[double bond, length as m-dash]C interactions (C5) to provide a C5-C6γ feature that stabilizes a planar geometry in the monomer unit. Two contiguous C5-C6γ features in the planar dimer implicate an unprecedented three-centre H-bond of the type C[double bond, length as m-dash]O⋯H(N)⋯SR2, while the trimer adopts two C5-C6γ features separated by a Ramachandran α-type backbone configuration. These low-energy conformers are fully characterized in the gas phase and support is presented for their existence in solution state.
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Affiliation(s)
- Zeynab Imani
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Venkateswara Rao Mundlapati
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Gildas Goldsztejn
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Jean-Pierre Baltaze
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Sylvie Robin
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France .,Faculté de Pharmacie, Université de Paris 75006 Paris France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Michel Mons
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - David J Aitken
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
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43
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Zhang Y, Yan X, Cao J, Weng P, Miao D, Li Z, Jiang YB. Turn Conformation of β-Amino Acid-Based Short Peptides Promoted by an Amidothiourea Moiety at C-Terminus. J Org Chem 2020; 85:9844-9849. [PMID: 32584574 DOI: 10.1021/acs.joc.0c01139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A C-terminal amidothiourea motif is shown to promote a β-turn-like folded conformation in a series of β-amino acid-based short peptides in both the solid state and solution phase by an intramolecular 11-membered ring hydrogen bond.
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Affiliation(s)
- Yanhan Zhang
- Department of Chemistry, College of Chemistry and Chemical Engineering, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Xiaosheng Yan
- Department of Chemistry, College of Chemistry and Chemical Engineering, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Jinlian Cao
- Department of Chemistry, College of Chemistry and Chemical Engineering, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Peimin Weng
- Department of Chemistry, College of Chemistry and Chemical Engineering, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Daiyu Miao
- Department of Chemistry, College of Chemistry and Chemical Engineering, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Zhao Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
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44
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Khatri B, Majumder P, Nagesh J, Penmatsa A, Chatterjee J. Increasing protein stability by engineering the n → π* interaction at the β-turn. Chem Sci 2020; 11:9480-9487. [PMID: 34094214 PMCID: PMC8161691 DOI: 10.1039/d0sc03060k] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abundant n → π* interactions between adjacent backbone carbonyl groups, identified by statistical analysis of protein structures, are predicted to play an important role in dictating the structure of proteins. However, experimentally testing the prediction in proteins has been challenging due to the weak nature of this interaction. By amplifying the strength of the n → π* interaction via amino acid substitution and thioamide incorporation at a solvent exposed β-turn within the GB1 proteins and Pin 1 WW domain, we demonstrate that an n → π* interaction increases the structural stability of proteins by restricting the ϕ torsion angle. Our results also suggest that amino acid side-chain identity and its rotameric conformation play an important and decisive role in dictating the strength of an n → π* interaction. Amino acid residues adopt a right-handed α-helical conformation with increasing strength of the n → π* interaction. We also demonstrate a direct consequence of n → π* interactions on enhancing the structural stability of proteins.![]()
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Puja Majumder
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
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45
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Darapaneni CM, Ghosh P, Ghosh T, Maayan G. Unique β‐Turn Peptoid Structures and Their Application as Asymmetric Catalysts. Chemistry 2020; 26:9573-9579. [DOI: 10.1002/chem.202000595] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 12/13/2022]
Affiliation(s)
| | - Pritam Ghosh
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Totan Ghosh
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Galia Maayan
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
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46
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Mammoli A, Coletti A, Ballarotto M, Riccio A, Carotti A, Grohmann U, Camaioni E, Macchiarulo A. New Insights from Crystallographic Data: Diversity of Structural Motifs and Molecular Recognition Properties between Groups of IDO1 Structures. ChemMedChem 2020; 15:891-899. [PMID: 32190988 DOI: 10.1002/cmdc.202000116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Indexed: 01/04/2023]
Abstract
A large number of crystallographic structures of IDO1 in different ligand-bound and -unbound states have been disclosed over the last decade. Yet, only a few of them have been exploited for structure-based drug design (SBDD) campaigns. In this study, we analyzed the structural motifs and molecular-recognition properties of three groups of IDO1 structures: 1) structures containing the heme group and inhibitors in the catalytic site; 2) heme-free structures of IDO1; 3) substrate-bound structures of IDO1. The results suggest that unrelated conformations of the enzyme have been solved with different ligand-induced changes of secondary motifs that localize even in regions remote from the catalytic site. Moreover, the study identified an uncharted region of molecular-recognition space covered by IDO1 binding sites that could guide the selection of diverse structures for additional SBDD studies aimed at the identification of novel lead compounds with differentiated chemical scaffolds.
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Affiliation(s)
- Andrea Mammoli
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Alice Coletti
- Department of Pharmacy, University of Chieti-Pescara, via dei Vestini n. 31, 66100, Chieti, Italy
| | - Marco Ballarotto
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Alessandra Riccio
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Ursula Grohmann
- Department of Experimental Medicine, University of Perugia, P.le Gambuli, 06132, Perugia, Italy
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
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47
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Bappy SS, Sultana S, Adhikari J, Mahmud S, Khan MA, Kibria KMK, Rahman MM, Shibly AZ. Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking confirmation against envelope protein of Chikungunya virus: a computational biology approach. J Biomol Struct Dyn 2020; 39:1139-1154. [PMID: 32037968 DOI: 10.1080/07391102.2020.1726815] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chikungunya virus (CHIKV) instigating Chikungunya fever is a global infective menace resulting in high fever, weakened joint-muscle pain, and brain inflammation. Inaccessibility and unavailability of effective drugs have led us to an uncertain arena when it comes to providing proper medical treatment to the affected people. In this study, authentic encroachment has been made concerning the peptide-based epitope vaccine designing against CHIKV. A Proteome-wide search was performed to locate a conserved portion among the accessible viral outer membrane proteins which showcase a remarkable immune response using specific immunoinformatics and docking simulation tools. Primarily, the most probable immunogenic envelope glycoproteins E1 and E2 were identified from the UniProt database depending on their antigenicity scores. Subsequently, we selected two distinctive sequences "SEDVYANTQLVLQRP" and "IMLLYPDHPTLLSYR" in both E1 and E2 glycoproteins respectively. These two sequences identified as the most potent T and B cell epitope-based peptides as they interacted with 6 and 7 HLA-I and 5 HLA-II molecules with an extremely low IC50 score that was verified by molecular docking. Moreover, the sequences possess no allergenicity and are certainly located outside the transmembrane region. In addition, the sequences exhibited 88.46% and 100.00% Conservancy, covering high population coverage of 89.49% to 94.74% and 60.51% to 88.87% respectively in endemic countries. The identified peptide SEDVYANTQLVLQRP and IMLLYPDHPTLLSYR can be utilized next for the development of peptide-based epitope vaccine contrary to CHIKV, so further documentations and experimentations like Antigen testing, Antigen production, Clinical trials are needed to prove the validity of it. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syed Shahariar Bappy
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Sorna Sultana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Juthi Adhikari
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh.,Bio-Bio-1 Research Foundation, Sangskriti Bikash Kendra Bhaban, Dhaka, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md Masuder Rahman
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
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48
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Marafon G, Moretto A, Zanuy D, Alemán C, Crisma M, Toniolo C. Effect on the Conformation of a Terminally Blocked, ( E) β,γ-Unsaturated δ-Amino Acid Residue Induced by Carbon Methylation. J Org Chem 2020; 85:1513-1524. [PMID: 31769989 DOI: 10.1021/acs.joc.9b02544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptides are well-known to play a fundamental therapeutic role and to represent building blocks for numerous useful biomaterials. Stabilizing their active 3D-structure by appropriate modifications remains, however, a challenge. In this study, we have expanded the available literature information on the conformational propensities of a promising backbone change of a terminally blocked δ-amino acid residue, a dipeptide mimic, by replacing its central amide moiety with an (E) Cβ═Cγ alkene unit. Specifically, we have examined by DFT calculations, X-ray diffraction in the crystalline state, and FT-IR absorption/NMR spectroscopies in solution the extended vs folded preferences of analogues of this prototype system either unmodified or possessing single or multiple methyl group substituents on each of its four -CH2-CH═CH-CH2- main-chain carbon atoms. The theoretical and experimental results obtained clearly point to the conclusion that increasing the number of adequately positioned methylations will enhance the preference of the original sequence to fold, thus opening interesting perspectives in the design of conformationally constrained peptidomimetics.
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Affiliation(s)
- Giulia Marafon
- Department of Chemical Sciences , University of Padova , 35131 Padova , Italy
| | - Alessandro Moretto
- Department of Chemical Sciences , University of Padova , 35131 Padova , Italy.,Institute of Biomolecular Chemistry , Padova Unit, CNR , 35131 Padova , Italy
| | - David Zanuy
- Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering , Universitat Polytècnica de Catalunya , 08019 Barcelona , Spain
| | - Carlos Alemán
- Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering , Universitat Polytècnica de Catalunya , 08019 Barcelona , Spain.,Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12 , 08028 Barcelona Spain
| | - Marco Crisma
- Institute of Biomolecular Chemistry , Padova Unit, CNR , 35131 Padova , Italy
| | - Claudio Toniolo
- Department of Chemical Sciences , University of Padova , 35131 Padova , Italy.,Institute of Biomolecular Chemistry , Padova Unit, CNR , 35131 Padova , Italy
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Migliore M, Bonvicini A, Tognetti V, Guilhaudis L, Baaden M, Oulyadi H, Joubert L, Ségalas-Milazzo I. Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study. Phys Chem Chem Phys 2020; 22:1611-1623. [PMID: 31894790 DOI: 10.1039/c9cp05776e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electronic circular dichroism is one of the most used spectroscopic techniques for peptide and protein structural characterization. However, while valuable experimental spectra exist for α-helix, β-sheet and random coil secondary structures, previous studies showed important discrepancies for β-turns, limiting their use as a reference for structural studies. In this paper, we simulated circular dichroism spectra for the best-characterized β-turns in peptides, namely types I, II, I' and II'. In particular, by combining classical molecular dynamics simulations and state-of-the-art quantum time-dependent density functional theory (with the polarizable embedding multiscale model) computations, two common electronic circular dichroism patterns were found for couples of β-turn types (namely, type I/type II' and type II/type I'), at first for a minimal di-peptide model (Ace-Ala-Ala-NHMe), but also for all sequences tested with non-aromatic residues in the central positions. On the other hand, as expected, aromatic substitution causes important perturbations to the previously found ECD patterns. Finally, by applying suitable approximations, these patterns were subsequently rationalized based on the exciton chirality rule. All these results provide useful predictions and pave the way for a possible experimental characterization of β-turns based on circular dichroism spectroscopy.
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Affiliation(s)
- Mattia Migliore
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Andrea Bonvicini
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Vincent Tognetti
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Laure Guilhaudis
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Hassan Oulyadi
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Isabelle Ségalas-Milazzo
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
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Yokoyama H, Mizutani R, Noguchi S, Hayashida N. Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab. Sci Rep 2019; 9:18494. [PMID: 31811216 PMCID: PMC6898713 DOI: 10.1038/s41598-019-54918-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/14/2019] [Indexed: 01/07/2023] Open
Abstract
The formation of the isoaspartate (isoAsp) is one of spontaneous degradation processes of proteins, affecting their stability and activity. Here, we report for the first time the crystal structures of an antibody Fab that contains isoAsp in the complementarity-determining region (CDR), along with biochemical studies to detect isoAsp. By comparing the elution profiles of cation-exchange chromatography, it was clarified that the antibody 64M-5 Fab is converted from the normal form to isoAsp form spontaneously and time-dependently under physiological conditions. The isoAsp residue was identified with tryptic peptide mapping, N-terminal sequencing, and the protein isoaspartyl methyltransferase assay. Based on the fluorescence quenching method, the isoAsp form of 64M-5 Fab shows a one order of magnitude lower binding constant for its dinucleotide ligand dT(6-4)T than the normal form. According to the structure of the isoAsp form, the conformation of CDR L1 is changed from the normal form to isoAsp form; the loss of hydrogen bonds involving the Asn28L side-chain, and structural conversion of the β-turn from type I to type II'. The formation of isoAsp leads to a large displacement of the side chain of His27dL, and decreased electrostatic interactions with the phosphate group of dT(6-4)T. Such structural changes should be responsible for the lower affinity of the isoAsp form for dT(6-4)T than the normal form. These findings may provide insight into neurodegenerative diseases (NDDs) and related diseases caused by misfolded proteins.
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Affiliation(s)
- Hideshi Yokoyama
- 0000 0001 0660 6861grid.143643.7Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641, Yamazaki, Noda, Chiba 278-8510 Japan
| | - Ryuta Mizutani
- 0000 0001 1516 6626grid.265061.6Graduate School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292 Japan
| | - Shuji Noguchi
- 0000 0000 9290 9879grid.265050.4Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510 Japan
| | - Naoki Hayashida
- 0000 0001 0660 7960grid.268397.1Division of Molecular Gerontology and Anti-Ageing Medicine, Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 Japan
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