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Kumar M, Rathore RS. Disallowed spots in protein structures. Biochim Biophys Acta Gen Subj 2023; 1867:130493. [PMID: 37865175 DOI: 10.1016/j.bbagen.2023.130493] [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: 05/29/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 10/23/2023]
Abstract
Ramachandran (ϕ, ψ) steric map was introduced in 1963 to describe available conformation space for protein structures. Subsequently, residues were observed in high-energy disallowed regions of the map. To unequivocally identify the locations of disallowed conformations of residues, we got 36 noise-free protein structures (resolution ≤1 Å, Rwork/Rfree ≤ 0.10). These stringent criteria were applied to rule out data or model errors or any crystallographic disorders. No disallowed conformation was found in the dataset. Further, we also examined disallowed conformations in a larger dataset (resolution ≤1.5 Å, devoid of any model errors, or disorders). The observed locations of disallowed residues are referred as disallowed spots. These spots include short loops of 3-5 residues, and locations where residues participate in disulfide bonding or intramolecular interactions or inter-molecular interactions with neighboring water, metals or ligands. Conformational sampling revealed that short loops in between secondary structures hardly have any opportunity to relieve from conformational strain. Residues involved in interactions, which provide energetic compensation for high-energy conformational states, were relieved from strain once the causative interaction was removed. The present study aims to identify disallowed spots in the native state of proteins, wherein residues are forced to be trapped in high-energy disallowed conformations. Moreover, it was also observed that pre-Pro, Ser, Asp, trans-Pro, Val, Asn & Gly have higher tendency to occur in disallowed conformation, which could be attributed to factors such as conformational restrictions, residue propensity of secondary structures and compensating sidechain and mainchain interactions, stabilizing turn-mimics.
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Affiliation(s)
- Mayank Kumar
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar 824236, India
| | - R S Rathore
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar 824236, India.
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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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Cui Y, Miao C, Chen W, Shang W, Qi Q, Zhou W, Wang X, Li Y, Yan Z, Jiang Y. Construction and protective efficacy of a novel Streptococcus pneumoniae fusion protein vaccine NanAT1-TufT1-PlyD4. Front Immunol 2022; 13:1043293. [PMID: 36389808 PMCID: PMC9659761 DOI: 10.3389/fimmu.2022.1043293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/17/2022] [Indexed: 01/19/2024] Open
Abstract
During the past decades, with the implementation of pneumococcal polysaccharide vaccine (PPV) and pneumococcal conjugate vaccines (PCVs), a dramatic reduction in vaccine type diseases and transmissions has occurred. However, it is necessary to develop a less expensive, serotype-independent pneumococcal vaccine due to the emergence of nonvaccine-type pneumococcal diseases and the limited effect of vaccines on colonization. As next-generation vaccines, conserved proteins, such as neuraminidase A (NanA), elongation factor Tu (Tuf), and pneumolysin (Ply), are promising targets against pneumococcal infections. Here, we designed and constructed a novel fusion protein, NanAT1-TufT1-PlyD4, using the structural and functional domains of full-length NanA, Tuf and Ply proteins with suitable linkers based on bioinformatics analysis and molecular cloning technology. Then, we tested whether the protein protected against focal and lethal pneumococcal infections and examined its potential protective mechanisms. The fusion protein NanAT1-TufT1-PlyD4 consists of 627 amino acids, which exhibits a relatively high level of thermostability, high stability, solubility and a high antigenic index without allergenicity. The purified fusion protein was used to subcutaneously immunize C57BL/6 mice, and NanAT1-TufT1-PlyD4 induced a strong and significant humoral immune response. The anti-NanAT1-TufT1-PlyD4 specific IgG antibody assays increased after the first immunization and reached the highest value at the 35th day. The results from in vitro experiments showed that anti-NanAT1-TufT1-PlyD4 antisera could inhibit the adhesion of Streptococcus pneumoniae (S. pneumoniae) to A549 cells. In addition, immunization with NanAT1-TufT1-PlyD4 significantly reduced S. pneumoniae colonization in the lung and decreased the damage to the lung tissues induced by S. pneumoniae infection. After challenge with a lethal dose of serotype 3 (NC_WCSUH32403), a better protection effect was observed with NanAT1-TufT1-PlyD4-immunized mice than with the separate full-length proteins and the adjuvant control; the survival rate was 50%, which met the standard of the marketed vaccine. Moreover, we showed that the humoral immune response and the Th1, Th2 and Th17-cellular immune pathways are involved in the immune protection of NanAT1-TufT1-PlyD4 to the host. Collectively, our results support that the novel fusion protein NanAT1-TufT1-PlyD4 exhibits extensive immune stimulation and is effective against pneumococcal challenges, and these properties are partially attributed to humoral and cellular-mediated immune responses.
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Affiliation(s)
- Yali Cui
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Laboratory Medicine, Meishan Women and Children’s Hospital, Alliance Hospital of West China Second University Hospital, Sichuan University, Meishan, China
| | - Chenglin Miao
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wen Chen
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Wenling Shang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qianqian Qi
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wei Zhou
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xia Wang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yingying Li
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ziyi Yan
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yongmei Jiang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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Mayank, Sidhu JS, Joshi G, Sindhu J, Kaur N, Singh N. Structural Diversity of D‐Alanine: D‐Alanine Ligase and Its Exploration in Development of Antibacterial Agents Against the Multi‐Variant Bacterial Infections. ChemistrySelect 2022. [DOI: 10.1002/slct.202104373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mayank
- Department of Chemistry Indian Institute of Technology Ropar Punjab 140001 India
- School of Pharmaceutical Sciences Lovely Professional University Phagwara India
| | - Jagpreet Singh Sidhu
- Department of Pharmaceutical Sciences and Natural Products School of Health Science Central University of Punjab Bathinda 151 001 India
| | - Gaurav Joshi
- School of Pharmacy Graphic Era Hill University Dehradun Uttarakhand India
| | - Jayant Sindhu
- Department of Chemistry COBS&H CCS Haryana Agricultural University Hisar 125004 India
| | - Navneet Kaur
- Department of Chemistry Panjab University Chandigarh 160014 India
| | - Narinder Singh
- Department of Chemistry Indian Institute of Technology Ropar Punjab 140001 India
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Affiliation(s)
- Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore.,School of Biological Sciences, Nanyang Technological University (NTU), Singapore
| | - Chandra Verma
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore.,School of Biological Sciences, Nanyang Technological University (NTU), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Tom Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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Hypervariability of accessible and inaccessible conformational space of proteins. Curr Res Struct Biol 2021; 3:229-238. [PMID: 34604793 PMCID: PMC8473459 DOI: 10.1016/j.crstbi.2021.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/22/2022] Open
Abstract
Proteins undergo motions in a range of amplitudes, from domain motions to backbone rotations, leading to changes in (φ,ψ) torsion angles and small-scale bond vibrations and angle bending. Here, we study the extent of variations in (φ,ψ) values in proteins and the effects of bond geometry variations due to vibrational motions in a protein on the accessible, (steric clash-free) (φ,ψ) space. We perform 1-fs timestep unconstrained molecular dynamics simulations on super-high-resolution protein structures. Extent of variations in bond geometry during the simulation is within acceptable ranges of bond lengths and angles. However, the steric clash-free (φ,ψ) space continuously changes as seen in bond geometry-specific (φ,ψ) steric maps at the residue level during simulations. (φ,ψ) regions that have steric clash at one timepoint can become steric clash-free at a different timepoint through minor adjustments to backbone bond lengths and angles. Also instances of (φ,ψ) transitions from the left to right half of the (φ,ψ) map in consecutive snapshots of the trajectory are seen. Although the two quadrants are separated by a steric clash-prone region, corresponding to a high-energy barrier, height of this barrier is lowered by adjusting the bond geometry such that a bridging region of steric clash-free, low-energy (φ,ψ) values is formed. We demonstrate the idea of dynamically varying nature of acceptable and accessible (φ,ψ) steric space in proteins, which has implications for protein folding; proteins could sample (φ,ψ) space which is originally considered to be inaccessible, during folding, through minor adjustments to their backbone bond geometry.
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