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Xu H, Mao B, Ni S, Xie X, Tang S, Wang Y, Zan X, Zheng Q, Huang W. Engineering Matrix-Free Drug Protein Nanoparticles with Promising Penetration through Biobarriers for Treating Corneal Neovascularization. ACS NANO 2024; 18:8209-8228. [PMID: 38452114 DOI: 10.1021/acsnano.3c12203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Protein drugs have been widely used in treating various clinical diseases because of their high specificity, fewer side effects, and favorable therapeutic effect, but they greatly suffer from their weak permeability through tissue barriers, high sensitivity to microenvironments, degradation by proteases, and rapid clearance by the immune system. Herein, we disrupted the standard protocol where protein drugs must be delivered as the cargo via a delivery system and innovatively developed a free entrapping matrix strategy by simply mixing bevacizumab (Beva) with zinc ions to generate Beva-NPs (Beva-Zn2+), where Beva is coordinatively cross-linked by zinc ions with a loading efficiency as high as 99.2% ± 0.41%. This strategy was universal to generating various protein NPs, with different metal ions (Cu2+, Fe3+, Mg2+, Sr2+). The synthetic conditions of Beva-NPs were optimized, and the generated mechanism was investigated in detail. The entrapment, releasing profile, and the bioactivities of released Beva were thoroughly studied. By using in situ doping of the fourth-generation polyamindoamine dendrimer (G4), the Beva-G4-NPs exhibited extended ocular retention and penetration through biobarriers in the anterior segment through transcellular and paracellular pathways, effectively inhibiting corneal neovascularization (CNV) from 91.6 ± 2.03% to 13.5 ± 1.87% in a rat model of CNV. This study contributes to engineering of protein NPs by using a facile strategy for overcoming the weaknesses of protein drugs and protein NPs, such as weak tissue barrier permeability, low encapsulation efficiency, poor loading capacity, and susceptibility to inactivation.
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Affiliation(s)
- Hongyan Xu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, People's Republic of China
- Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Bangxun Mao
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, People's Republic of China
| | - Shulan Ni
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, People's Republic of China
- Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Xiaoling Xie
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, People's Republic of China
| | - Sicheng Tang
- Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Yang Wang
- Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Xingjie Zan
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, People's Republic of China
- Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Qinxiang Zheng
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, People's Republic of China
- The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, Ningbo 315000, People's Republic of China
| | - Wenjuan Huang
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, People's Republic of China
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2
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D'Arminio N, Ruggiero V, Pierri G, Marabotti A, Tedesco C. Emerging role of carbonyl-carbonyl interactions in the classification of beta turns. Protein Sci 2024; 33:e4868. [PMID: 38100281 PMCID: PMC10806932 DOI: 10.1002/pro.4868] [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: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Carbonyl-carbonyl interactions in peptides and proteins attracted considerable interest in recent years. Here, we report a survey of carbonyl-carbonyl interactions in cyclic peptides, depsipeptides, peptoids and discuss the relationship between backbone torsion angles and CO∙∙∙CO distances. In general, φ values in the range between -40° and -90° and between 40° and 90° correspond to CO∙∙∙CO distances below 3.22 Å. By extending the analysis of carbonyl-carbonyl interactions in different types of beta turns in proteins, we also highlight the role of direct or reciprocal carbonyl-carbonyl interactions in stabilizing the beta turn conformation for each specific type. We confirmed the new type II beta turn, detected by Dunbrack and coworkers, and named Pa, and detect the presence of a direct carbonyl-carbonyl interaction between the second and third residues of the turn. We also evidenced the existence of another new type II beta turn, named pA (following Dunbrack's notation), which represents the alternative conformation of Pa with opposite φ and ψ values and is characterized by a direct carbonyl-carbonyl interaction between the second and third residues of the turn. Finally, we show that the occurrence of CO∙∙∙CO interactions could be also advocated to explain from a chemical point of view the diversity of turn types.
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Affiliation(s)
- Nancy D'Arminio
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Valentina Ruggiero
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
- Present address:
Department of PharmacyUniversity of SalernoFiscianoItaly
| | - Giovanni Pierri
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Anna Marabotti
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Consiglia Tedesco
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
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Martins C, Diharce J, Nadaradjane AA, de Brevern AG. Evaluation of the Potential Impact of In Silico Humanization on V HH Dynamics. Int J Mol Sci 2023; 24:14586. [PMID: 37834033 PMCID: PMC10572902 DOI: 10.3390/ijms241914586] [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: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Camelids have the peculiarity of having classical antibodies composed of heavy and light chains as well as single-chain antibodies. They have lost their light chains and one heavy-chain domain. This evolutionary feature means that their terminal heavy-chain domain, VH, called VHH here, has no partner and forms an independent domain. The VHH is small and easy to express alone; it retains thermodynamic and interaction properties. Consequently, VHHs have garnered significant interest from both biotechnological and pharmaceutical perspectives. However, due to their origin in camelids, they cannot be used directly on humans. A humanization step is needed before a possible use. However, changes, even in the constant parts of the antibodies, can lead to a loss of quality. A dedicated tool, Llamanade, has recently been made available to the scientific community. In a previous paper, we already showed the different types of VHH dynamics. Here, we have selected a representative VHH and tested two humanization hypotheses to accurately assess the potential impact of these changes. This example shows that despite the non-negligible change (1/10th of residues) brought about by humanization, the effect is not drastic, and the humanized VHH retains conformational properties quite similar to those of the camelid VHH.
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Affiliation(s)
- Carla Martins
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
| | - Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
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4
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Atiya A, Batra S, Mohammad T, Alorfi NM, Abdulmonem WA, Alhumaydhi FA, Ashraf GM, Baeesa SS, Elasbali AM, Shahwan M. Desmodin and isopongachromene as potential inhibitors of cyclin-dependent kinase 5: phytoconstituents targeting anticancer and neurological therapy. J Biomol Struct Dyn 2023; 41:8042-8052. [PMID: 36184739 DOI: 10.1080/07391102.2022.2128877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/20/2022] [Indexed: 10/07/2022]
Abstract
Cyclin-dependent kinase 5 (CDK5) is a proline-directed serine-threonine protein kinase vital for neuronal cell cycle arrest and differentiation. It activates by binding with p35 and p39 and is important for the functioning of the nervous system. A growing body of evidence suggests that CDK5 contributes to the onset and progression of neurodegeneration and tumorigenesis and represents itself as a potential therapeutic target. Our research illustrates virtual screening of phytochemicals from the IMPPAT (Indian Medicinal Plants, Phytochemistry and Therapeutics) library to search for potential inhibitors of CDK5. Initially, the compounds from the parent library were filtered out via their physicochemical properties following the Lipinski rule of five. Then sequentially, molecular docking-based virtual screening, PAINS filter, ADMET, PASS analysis, and molecular dynamics (MD) simulation were done using various computational tools to rule out adversities that can cause hindrances in the identification of potential inhibitors of CDK5. Finally, two compounds were selected via the extensive screening showing significant binding with CDK5 ATP-binding pocket and ultimately were selected as potent ATP-competitive inhibitors of CDK5. Finally, we propose that the elucidated compounds Desmodin and Isopongachromene can be used further in the drug discovery process and act as therapeutics in the medical industry to treat certain complex diseases, including cancer and neurodegeneration.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
| | - Shivani Batra
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Nasser M Alorfi
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraidah, Kingdom of Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraidah, Saudi Arabia
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saleh S Baeesa
- Division of Neurosurgery, College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Moyad Shahwan
- College of Pharmacy, Ajman University, Abha, United Arab Emirates
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Abha, United Arab Emirates
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5
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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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6
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Structural and Dynamic Differences between Calreticulin Mutants Associated with Essential Thrombocythemia. Biomolecules 2023; 13:biom13030509. [PMID: 36979444 PMCID: PMC10046389 DOI: 10.3390/biom13030509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023] Open
Abstract
Essential thrombocythemia (ET) is a blood cancer. ET is characterized by an overproduction of platelets that can lead to thrombosis formation. Platelet overproduction occurs in megakaryocytes through a signaling pathway that could involve JAK2, MPL, or CALR proteins. CALR mutations are associated with 25–30% of ET patients; CALR variants must be dimerized to induce ET. We classified these variants into five classes named A to E; classes A and B are the most frequent classes in patients with ET. The dynamic properties of these five classes using structural models of CALR’s C-domain were analyzed using molecular dynamics simulations. Classes A, B, and C are associated with frameshifts in the C-domain. Their dimers can be stable only if a disulfide bond is formed; otherwise, the two monomers repulse each other. Classes D and E cannot be stable as dimers due to the absence of disulfide bonds. Class E and wild-type CALR have similar dynamic properties. These results suggest that the disulfide bond newly formed in classes A, B, and C may be essential for the pathogenicity of these variants. They also underline that class E cannot be directly related to ET but corresponds to human polymorphisms.
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Yan J, Zheng Z. Discovery of Highly Potent CRBN Ligands and Insight into Their Binding Mode through Molecular Docking and Molecular Dynamics Simulations. ChemMedChem 2023; 18:e202200573. [PMID: 36750890 DOI: 10.1002/cmdc.202200573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/21/2022] [Indexed: 02/09/2023]
Abstract
Cereblon (CRBN) is a substrate receptor of E3 ubiquitin ligase as well as the target of thalidomide and lenalidomide, plays a vital role in endogenous protein degradation. In this article, two series of compounds with novel structure were designed, synthesized and evaluated against CRBN. YJ1b, designed based on our previous finding, shown strong binding affinity toward CRBN (IC50 =0.206 μM) by forming a salt bridge interaction with amino acid residue Glu377 of CRBN, it was 13-fold compared with that of lenalidomide (IC50 =2.694 μM) in TR-FRET assay. YJ2c and YJ2h, two analogs of YJ1b, also exhibit high binding affinity toward CRBN (IC50 =0.211 μM and IC50 =0.282 μM, respectively). While, molecular docking and 100 ns molecular dynamic simulation studies were conducted to insight into the unique binding mode of YJ1b, YJ2c and YJ2e toward CRBN. The new compounds with special binding mode in this article may serve for the further optimization and discovery of novel high potent CRBN ligands.
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Affiliation(s)
- Jian Yan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Zhibing Zheng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
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8
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Gaur NK, Ghosh B, Goyal VD, Kulkarni K, Makde RD. Evolutionary conservation of protein dynamics: insights from all-atom molecular dynamics simulations of 'peptidase' domain of Spt16. J Biomol Struct Dyn 2023; 41:1445-1457. [PMID: 34971347 DOI: 10.1080/07391102.2021.2021990] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Protein function is encoded in its sequence, manifested in its three-dimensional structure, and facilitated by its dynamics. Studies have suggested that protein structures with higher sequence similarity could have more similar patterns of dynamics. However, such studies of protein dynamics within and across protein families typically rely on coarse-grained models, or approximate metrics like crystallographic B-factors. This study uses µs scale molecular dynamics (MD) simulations to explore the conservation of dynamics among homologs of ∼50 kDa N-terminal module of Spt16 (Spt16N). Spt16N from Saccharomyces cerevisiae (Sc-Spt16N) and three of its homologs with 30-40% sequence identities were available in the PDB. To make our data-set more comprehensive, the crystal structure of an additional homolog (62% sequence identity with Sc-Spt16N) was solved at 1.7 Å resolution. Cumulative MD simulations of 6 µs were carried out on these Spt16N structures and on two additional protein structures with varying degrees of similarity to it. The simulations revealed that correlation in patterns of backbone fluctuations vary linearly with sequence identity. This trend could not be inferred using crystallographic B-factors. Further, normal mode analysis suggested a similar pattern of inter-domain (inter-lobe) motions not only among Spt16N homologs, but also in the M24 peptidase structure. On the other hand, MD simulation results highlighted conserved motions that were found unique for Spt16N protein, this along with electrostatics trends shed light on functional aspects of Spt16N.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neeraj K Gaur
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India.,Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Biplab Ghosh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Venuka Durani Goyal
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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9
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General Trends of the Camelidae Antibody V HHs Domain Dynamics. Int J Mol Sci 2023; 24:ijms24054511. [PMID: 36901942 PMCID: PMC10003728 DOI: 10.3390/ijms24054511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Conformational flexibility plays an essential role in antibodies' functional and structural stability. They facilitate and determine the strength of antigen-antibody interactions. Camelidae express an interesting subtype of single-chain antibody, named Heavy Chain only Antibody. They have only one N-terminal Variable domain (VHH) per chain, composed of Frameworks (FRs) and Complementarity Determining regions (CDRs) like their VH and VL counterparts in IgG. Even when expressed independently, VHH domains display excellent solubility and (thermo)stability, which helps them to retain their impressive interaction capabilities. Sequence and structural features of VHH domains contributing to these abilities have already been studied compared to classical antibodies. To have the broadest view and understand the changes in dynamics of these macromolecules, large-scale molecular dynamics simulations for a large number of non-redundant VHH structures have been performed for the first time. This analysis reveals the most prevalent movements in these domains. It reveals the four main classes of VHHs dynamics. Diverse local changes were observed in CDRs with various intensities. Similarly, different types of constraints were observed in CDRs, while FRs close to CDRs were sometimes primarily impacted. This study sheds light on the changes in flexibility in different regions of VHH that may impact their in silico design.
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Nadaradjane AA, Diharce J, Rebehmed J, Cadet F, Gardebien F, Gelly JC, Etchebest C, de Brevern AG. Quality assessment of V HH models. J Biomol Struct Dyn 2023; 41:13287-13301. [PMID: 36752327 DOI: 10.1080/07391102.2023.2172613] [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: 10/13/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Heavy Chain Only Antibodies are specific to Camelid species. Despite the lack of the light chain variable domain, their heavy chain variable domain (VH) domain, named VHH or nanobody, has promising potential applications in research and therapeutic fields. The structural study of VHH is therefore of great interest. Unfortunately, considering the huge amount of sequences that might be produced, only about one thousand of VHH experimental structures are publicly available in the Protein Data Bank, implying that structural model prediction of VHH is a necessary alternative to obtaining 3D information besides its sequence. The present study aims to assess and compare the quality of predictions from different modelling methodologies. Established comparative & homology modelling approaches to recent Deep Learning-based modelling strategies were applied, i.e. Modeller using single or multiple structural templates, ModWeb, SwissModel (with two evaluation schema), RoseTTAfold, AlphaFold 2 and NanoNet. The prediction accuracy was evaluated using RMSD, TM-score, GDT-TS, GDT-HA and Protein Blocks distance metrics. Besides the global structure assessment, we performed specific analyses of Frameworks and CDRs structures. We observed that AlphaFold 2 and especially NanoNet performed better than the other evaluated softwares. Importantly, we performed molecular dynamics simulations of an experimental structure and a NanoNet predicted model of a VHH in order to compare the global structural flexibility and local conformations using Protein Blocks. Despite rather similar structures, substantial differences in dynamical properties were observed, which underlies the complexity of the task of model evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese, American University, Beirut, Lebanon
| | - Frédéric Cadet
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
- Artificial Intelligence Department, PEACCEL, Paris, France
| | - Fabrice Gardebien
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Catherine Etchebest
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Alexandre G de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
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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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V HH Structural Modelling Approaches: A Critical Review. Int J Mol Sci 2022; 23:ijms23073721. [PMID: 35409081 PMCID: PMC8998791 DOI: 10.3390/ijms23073721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/20/2022] Open
Abstract
VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared to classical mammalian antibodies. The number of experimentally solved VHH structures has significantly improved recently, which is of great help, because it offers the ability to directly work on 3D structures to humanise or improve them. Unfortunately, most VHHs do not have 3D structures. Thus, it is essential to find alternative ways to get structural information. The methods of structure prediction from the primary amino acid sequence appear essential to bypass this limitation. This review presents the most extensive overview of structure prediction methods applied for the 3D modelling of a given VHH sequence (a total of 21). Besides the historical overview, it aims at showing how model software programs have been shaping the structural predictions of VHHs. A brief explanation of each methodology is supplied, and pertinent examples of their usage are provided. Finally, we present a structure prediction case study of a recently solved VHH structure. According to some recent studies and the present analysis, AlphaFold 2 and NanoNet appear to be the best tools to predict a structural model of VHH from its sequence.
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13
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Analysis of Integrin α IIb Subunit Dynamics Reveals Long-Range Effects of Missense Mutations on Calf Domains. Int J Mol Sci 2022; 23:ijms23020858. [PMID: 35055046 PMCID: PMC8776176 DOI: 10.3390/ijms23020858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/23/2021] [Accepted: 12/30/2021] [Indexed: 11/17/2022] Open
Abstract
Integrin αIIbβ3, a glycoprotein complex expressed at the platelet surface, is involved in platelet aggregation and contributes to primary haemostasis. Several integrin αIIbβ3 polymorphisms prevent the aggregation that causes haemorrhagic syndromes, such as Glanzmann thrombasthenia (GT). Access to 3D structure allows understanding the structural effects of polymorphisms related to GT. In a previous analysis using Molecular Dynamics (MD) simulations of αIIbCalf-1 domain structure, it was observed that GT associated with single amino acid variation affects distant loops, but not the mutated position. In this study, experiments are extended to Calf-1, Thigh, and Calf-2 domains. Two loops in Calf-2 are unstructured and therefore are modelled expertly using biophysical restraints. Surprisingly, MD revealed the presence of rigid zones in these loops. Detailed analysis with structural alphabet, the Proteins Blocks (PBs), allowed observing local changes in highly flexible regions. The variant P741R located at C-terminal of Calf-1 revealed that the Calf-2 presence did not affect the results obtained with isolated Calf-1 domain. Simulations for Calf-1 + Calf-2, and Thigh + Calf-1 variant systems are designed to comprehend the impact of five single amino acid variations in these domains. Distant conformational changes are observed, thus highlighting the potential role of allostery in the structural basis of GT.
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Craveur P, Narwani TJ, Srinivasan N, Gelly JC, Rebehmed J, de Brevern AG. Shaking the β-Bulges. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:14-18. [PMID: 34115590 DOI: 10.1109/tcbb.2021.3088444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
β-bulges are irregularities inside the β-sheets. They represent more than 3 percent of the protein residues, i.e., they are as frequent as 3.10 helices. In terms of evolution, β-bulges are not more conserved than any other local protein conformations within homologous protein structures. In a first of its kind study, we have investigated the dynamical behaviour of β-bulges using the largest known set of protein molecular dynamics simulations. We observed that more than 50 percent of the existing β-bulges in protein crystal structures remained stable during dynamics while more than1/6th were not stable at all and disappeared entirely. Surprisingly, 1.1 percent of β-bulges that appeared remained stable. β-bulges have been categorized in different subtypes. The most common β-bulges' types are the smallest insertion in β-strands (namely AC and AG); they are found as stable as the whole β-bulges dataset. Low occurring types (namely PC and AS), that have the largest insertions, are significantly more stable than expected. Thus, this pioneer study allowed to precisely quantify the stability of the β-bulges, demonstrating their structural robustness, with few unexpected cases raising structural questions.
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de Brevern AG. Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet. Biomolecules 2020; 10:biom10071080. [PMID: 32698546 PMCID: PMC7408373 DOI: 10.3390/biom10071080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022] Open
Abstract
Intrinsically-disordered protein (IDP) characterization was an amazing change of paradigm in our classical sequence-structure-function theory. Moreover, IDPs are over-represented in major disease pathways and are now often targeted using small molecules for therapeutic purposes. This has had created a complex continuum from order-that encompasses rigid and flexible regions-to disorder regions; the latter being not accessible through classical crystallographic methodologies. In X-ray structures, the notion of order is dictated by access to resolved atom positions, providing rigidity and flexibility information with low and high experimental B-factors, while disorder is associated with the missing (non-resolved) residues. Nonetheless, some rigid regions can be found in disorder regions. Using ensembles of IDPs, their local conformations were analyzed in the light of a structural alphabet. An entropy index derived from this structural alphabet allowed us to propose a continuum of states from rigidity to flexibility and finally disorder. In this study, the analysis was extended to comparing these results to disorder predictions, underlying a limited correlation, and so opening new ideas to characterize and predict disorder.
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Affiliation(s)
- Alexandre G de Brevern
- INSERM, UMR_S 1134, DSIMB, Univ Paris, INTS, Laboratoire d'Excellence GR-Ex, 75015 Paris, France
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Srivastav AK, Gupta SK, Kumar U. A molecular simulation approach towards the development of universal nanocarriers by studying the pH- and electrostatic-driven changes in the dynamic structure of albumin. RSC Adv 2020; 10:13451-13459. [PMID: 35492989 PMCID: PMC9051469 DOI: 10.1039/d0ra00803f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/14/2020] [Indexed: 01/15/2023] Open
Abstract
To explore the intramolecular interactions of protein, and its folding and unfolding mechanisms, we performed a simulation-based comparative study on albumin at different ionic strengths and pH. In this study, we performed molecular dynamics (MD) simulation for bovine serum albumin (BSA) at five different concentrations of NaCl (10, 20, 30, 40 and 50 mM), and five different pH values (2.0, 3.5, 4.3, 7.4, and 9.0). Herein, our aim was to unravel the effects of both pH and ionic strength on the conformations of the serum albumin structure. Our results indicate the effects of physicochemical factors in promoting conformational changes in the albumin structure, unlocking the hydrophobic sequences for hydrophobic drug binding. The BSA structure showed similarity to its native state in the pH range of 4.5 to 7.4 and at various ionic concentrations of NaCl. In the pH range of 3.5 to 4.5, the BSA structure showed denaturation in a controlled manner, which caused significant conformational changes in the molecular position of its hydrophobic amino acid residues. The resultant 3D structure gives insight into the amino acid trajectories. High denaturation and unstable behavior in the structural and conformational changes of the protein structure were observed at pH 2.0 and pH 9.0. We believe that these results and conditions will be helpful in the development of protein-based universal nanocarriers for the encapsulation of both hydrophilic and hydrophobic drugs. Role of pH and electrostatic charges on the conformations and dynamics of albumin structure by molecular dynamic study.![]()
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Affiliation(s)
| | - Sanjeev K. Gupta
- Computational Materials and Nanoscience Group
- Department of Physics
- St. Xavier's College
- Ahmedabad 380009
- India
| | - Umesh Kumar
- School of Nano Sciences
- Central University of Gujarat
- Gandhinagar
- India
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Faure G, Joseph AP, Craveur P, Narwani TJ, Srinivasan N, Gelly JC, Rebehmed J, de Brevern AG. iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach. SOURCE CODE FOR BIOLOGY AND MEDICINE 2019; 14:5. [PMID: 31700529 PMCID: PMC6825713 DOI: 10.1186/s13029-019-0075-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/14/2019] [Indexed: 11/10/2022]
Abstract
Background Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. Multiple approaches have been developed to perform such task and are often based on structural superimposition deduced from sequence alignment, which does not take into account structural features. Our methodology is based on the use of a Structural Alphabet (SA), i.e. a library of 3D local protein prototypes able to approximate protein backbone. The interest of a SA is to translate into 1D sequences into the 3D structures. Results We used Protein blocks (PB), a widely used SA consisting of 16 prototypes, each representing a conformation of the pentapeptide skeleton defined in terms of dihedral angles. Proteins are described using PB from which we have previously developed a sequence alignment procedure based on dynamic programming with a dedicated PB Substitution Matrix. We improved the procedure with a specific two-step search: (i) very similar regions are selected using very high weights and aligned, and (ii) the alignment is completed (if possible) with less stringent parameters. Our approach, iPBA, has shown to perform better than other available tools in benchmark tests. To facilitate the usage of iPBA, we designed and implemented iPBAvizu, a plugin for PyMOL that allows users to run iPBA in an easy way and analyse protein superimpositions. Conclusions iPBAvizu is an implementation of iPBA within the well-known and widely used PyMOL software. iPBAvizu enables to generate iPBA alignments, create and interactively explore structural superimposition, and assess the quality of the protein alignments.
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Affiliation(s)
- Guilhem Faure
- INSERM, U 1134, DSIMB, Univ Paris, Univ de la Réunion, Univ des Antilles, F-75739 Paris, France
| | - Agnel Praveen Joseph
- INSERM, U 1134, DSIMB, Univ Paris, Univ de la Réunion, Univ des Antilles, F-75739 Paris, France.,INSERM UMR_S 1134, DSIMB, Université de Paris, Institut National de la Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, F-75739, Paris cedex 15, France.,Laboratoire d'Excellence GR-Ex, F-75739 Paris, France.,4Birkbeck College, University of London, London, UK
| | - Pierrick Craveur
- INSERM, U 1134, DSIMB, Univ Paris, Univ de la Réunion, Univ des Antilles, F-75739 Paris, France.,INSERM UMR_S 1134, DSIMB, Université de Paris, Institut National de la Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, F-75739, Paris cedex 15, France.,Laboratoire d'Excellence GR-Ex, F-75739 Paris, France.,5Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Tarun J Narwani
- INSERM, U 1134, DSIMB, Univ Paris, Univ de la Réunion, Univ des Antilles, F-75739 Paris, France.,INSERM UMR_S 1134, DSIMB, Université de Paris, Institut National de la Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, F-75739, Paris cedex 15, France.,Laboratoire d'Excellence GR-Ex, F-75739 Paris, France
| | | | - Jean-Christophe Gelly
- INSERM, U 1134, DSIMB, Univ Paris, Univ de la Réunion, Univ des Antilles, F-75739 Paris, France.,INSERM UMR_S 1134, DSIMB, Université de Paris, Institut National de la Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, F-75739, Paris cedex 15, France.,Laboratoire d'Excellence GR-Ex, F-75739 Paris, France
| | - Joseph Rebehmed
- INSERM, U 1134, DSIMB, Univ Paris, Univ de la Réunion, Univ des Antilles, F-75739 Paris, France.,INSERM UMR_S 1134, DSIMB, Université de Paris, Institut National de la Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, F-75739, Paris cedex 15, France.,Laboratoire d'Excellence GR-Ex, F-75739 Paris, France.,7Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, Univ Paris, Univ de la Réunion, Univ des Antilles, F-75739 Paris, France.,INSERM UMR_S 1134, DSIMB, Université de Paris, Institut National de la Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, F-75739, Paris cedex 15, France.,Laboratoire d'Excellence GR-Ex, F-75739 Paris, France
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