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Feng M, Chan KC, Zhong Q, Zhou R. In silico design of high-affinity antigenic peptides for HLA-B44. Int J Biol Macromol 2024; 267:131356. [PMID: 38574928 DOI: 10.1016/j.ijbiomac.2024.131356] [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: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Cancer cell-killing by CD8+ T cells demands effective tumor antigen presentation by human leukocyte antigen class I (HLA-I) molecules. Screening and designing highly immunogenic neoantigens require quantitative computations to reliably predict HLA-peptide binding affinities. Here, with all-atom molecular dynamics (MD) simulations and free energy perturbation (FEP) methods, we design a collection of antigenic peptide candidates through in silico mutagenesis studies on immunogenic neoantigens, yielding enhanced binding affinities to HLA-B*44:02. In-depth structural dissection shows that introducing positively charged residues such as arginine to position 6 or lysine to position 7 of the candidates triggers conformational shifts in both peptides and the antigen-binding groove of the HLA, following the "induced-fit" mechanism. Enhancement in binding affinities compared to the wild-type was found in three out of five mutated candidates. The HLA pocket, capable of accommodating positively charged residues in positions from 5 to 7, is designated as the "dynamic pocket". Taken together, we showcase an effective structure-based binding affinity optimization framework for antigenic peptides of HLA-B*44:02 and underscore the importance of dynamic nature of the antigen-binding groove in concert with the anchoring motifs. This work provides structural insights for rational design of favorable HLA-peptide bindings and future developments in neoantigen-based therapeutics.
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Affiliation(s)
- Mei Feng
- Lanzhou Center for Theoretical Physics, Key Laboratory of Theoretical Physics of Gansu Province, Lanzhou University, Lanzhou, Gansu 730000, China; Institute of Quantitative Biology, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China; Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China
| | - Kevin C Chan
- Institute of Quantitative Biology, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China; Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China
| | - Qinglu Zhong
- Institute of Quantitative Biology, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China; Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China; Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China; The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Department of Chemistry, Columbia University, New York, NY 10027, USA.
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Torrents de la Peña A, Sewall LM, de Paiva Froes Rocha R, Jackson AM, Pratap PP, Bangaru S, Cottrell CA, Mohanty S, Shaw AC, Ward AB. Increasing sensitivity of antibody-antigen interactions using photo-cross-linking. CELL REPORTS METHODS 2023; 3:100509. [PMID: 37426749 PMCID: PMC10326447 DOI: 10.1016/j.crmeth.2023.100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/12/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023]
Abstract
Understanding antibody-antigen interactions in a polyclonal immune response in humans and animal models is critical for rational vaccine design. Current approaches typically characterize antibodies that are functionally relevant or highly abundant. Here, we use photo-cross-linking and single-particle electron microscopy to increase antibody detection and unveil epitopes of low-affinity and low-abundance antibodies, leading to a broader structural characterization of polyclonal immune responses. We employed this approach across three different viral glycoproteins and showed increased sensitivity of detection relative to currently used methods. Results were most noticeable in early and late time points of a polyclonal immune response. Additionally, the use of photo-cross-linking revealed intermediate antibody binding states and demonstrated a distinctive way to study antibody binding mechanisms. This technique can be used to structurally characterize the landscape of a polyclonal immune response of patients in vaccination or post-infection studies at early time points, allowing for rapid iterative design of vaccine immunogens.
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Affiliation(s)
- Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Leigh M. Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rebeca de Paiva Froes Rocha
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Abigail M. Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Payal P. Pratap
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A. Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Subhasis Mohanty
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Albert C. Shaw
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Becerra A, Muñoz-Velasco I, Aguilar-Cámara A, Cottom-Salas W, Cruz-González A, Vázquez-Salazar A, Hernández-Morales R, Jácome R, Campillo-Balderas JA, Lazcano A. Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein. Sci Rep 2022; 12:936. [PMID: 35042962 PMCID: PMC8766472 DOI: 10.1038/s41598-022-04976-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/04/2022] [Indexed: 11/24/2022] Open
Abstract
Low complexity regions (LCRs) are protein sequences formed by a set of compositionally biased residues. LCRs are extremely abundant in cellular proteins and have also been reported in viruses, where they may partake in evasion of the host immune system. Analyses of 28,231 SARS-CoV-2 whole proteomes and of 261,051 spike protein sequences revealed the presence of four extremely conserved LCRs in the spike protein of several SARS-CoV-2 variants. With the exception of Iota, where it is absent, the Spike LCR-1 is present in the signal peptide of 80.57% of the Delta variant sequences, and in other variants of concern and interest. The Spike LCR-2 is highly prevalent (79.87%) in Iota. Two distinctive LCRs are present in the Delta spike protein. The Delta Spike LCR-3 is present in 99.19% of the analyzed sequences, and the Delta Spike LCR-4 in 98.3% of the same set of proteins. These two LCRs are located in the furin cleavage site and HR1 domain, respectively, and may be considered hallmark traits of the Delta variant. The presence of the medically-important point mutations P681R and D950N in these LCRs, combined with the ubiquity of these regions in the highly contagious Delta variant opens the possibility that they may play a role in its rapid spread.
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Affiliation(s)
- Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Israel Muñoz-Velasco
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | | | - Wolfgang Cottom-Salas
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Escuela Nacional Preparatoria, Plantel 8 Miguel E. Schulz, Universidad Nacional Autónoma de México, 01600, Mexico City, Mexico
| | - Adrián Cruz-González
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Alberto Vázquez-Salazar
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
| | | | - Rodrigo Jácome
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | | | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
- El Colegio Nacional, 06470, Mexico City, Mexico.
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Li X, Bai L, Zhang Y, Wang Y, Shi Y, Liu H. Novel GLP-1/anti-apolipoprotein B bifunctional fusion protein alleviates diabetes and diabetic complications in combination with low-intensity ultrasound. Life Sci 2021; 278:119549. [PMID: 33933459 DOI: 10.1016/j.lfs.2021.119549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/09/2021] [Accepted: 04/17/2021] [Indexed: 12/16/2022]
Abstract
AIMS To engineer and screen a novel GLP-1/anti-apolipoprotein B (apoB) bifunctional fusion protein with therapeutic potential on alleviating diabetes and diabetic complication in combination with low-intensity ultrasound. MAIN METHODS Anti-apoB antibodies were screened by phage display technology and further fused to mutated GLP-1 (7-37) via light or heavy fusion to generate bifunctional fusion protein (termed aBG). The optimal design of aBG fusion protein was further confirmed by in vitro epitope competition assay and cAMP accumulation assay. Subsequently, chronic study in DIO mice were subjected to assess the long-term efficacy of screened fusion protein. KEY FINDINGS The selected GLP-1/anti-apoB fusion protein, aBG-8, exerted either the highest binding affinities for GLP-1R and apoB, or the greatest LDL-C uptake capacity and GLP-1R activation activity. After 60-day treatment in DIO mice, aBG-8 was proved to exert the promising improvement on hyperglycemia, hyperlipidemia, and obesity in DIO mice. Furthermore, combined therapy of aBG-8 and low-intensity ultrasound could accelerate skin wound closure in diabetic mice. SIGNIFICANCE A novel long-lasting bifunctional fusion molecule, aBG-8, was designed with the enormous potential on alleviating diabetes and diabetic complications in combination with low-intensity ultrasound.
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Affiliation(s)
- Xing Li
- Ultrasound Department of The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang Province, China
| | - Lianjie Bai
- Ultrasound Department of The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang Province, China
| | - Yinghui Zhang
- Ultrasound Department of The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang Province, China
| | - Ying Wang
- Ultrasound Department of The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang Province, China
| | - Yang Shi
- Ultrasound Department of The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang Province, China
| | - Huilin Liu
- Ultrasound Department of The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang Province, China.
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Feng M, Song Y, Chen SH, Zhang Y, Zhou R. Molecular mechanism of secreted amyloid-β precursor protein in binding and modulating GABA BR1a. Chem Sci 2021; 12:6107-6116. [PMID: 33996007 PMCID: PMC8098695 DOI: 10.1039/d0sc06946a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A recent phenomenal study discovered that the extension domain of secreted amyloid-β precursor protein (sAPP) can bind to the intrinsically disordered sushi 1 domain of the γ-aminobutyric acid type B receptor subunit 1a (GABABR1a) and modulate its synaptic transmission. The work provided an important structural foundation for the modulation of GABABR1a; however, the detailed molecular interaction mechanism, crucial for future drug design, remains elusive. Here, we further investigated the dynamical interactions between sAPP peptides and the natively unstructured sushi 1 domain using all-atom molecular dynamics simulations, for both the 17-residue sAPP peptide (APP 17-mer) and its minimally active 9 residue segment (APP 9-mer). We then explored mutations of the APP 9-mer with rigorous free energy perturbation (FEP) calculations. Our in silico mutagenesis studies revealed key residues (D4, W6, and W7) responsible for the binding with the sushi 1 domain. More importantly, one double mutation based on different vertebrate APP sequences from evolution exhibited a stronger binding (ΔΔG = −1.91 ± 0.66 kcal mol−1), indicating a potentially enhanced GABABR1a modulator. These large-scale simulations may provide new insights into the binding mechanism between sAPP and the sushi 1 domain, which could open new avenues in the development of future GABABR1a-specific therapeutics. A recent phenomenal study discovered that the extension domain of secreted amyloid-β precursor protein (sAPP) can bind to the intrinsically disordered sushi 1 domain of the γ-aminobutyric acid type B receptor subunit 1a (GABABR1a) and modulate its synaptic transmission.![]()
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Affiliation(s)
- Mei Feng
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, Department of Physics, Zhejiang University Hangzhou 310027 China .,Lanzhou Center for Theoretical Physics, Key Laboratory of Theoretical Physics of Gansu Province, Lanzhou University Lanzhou Gansu 730000 China
| | - Yi Song
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, Department of Physics, Zhejiang University Hangzhou 310027 China
| | - Serena H Chen
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory Oak Ridge TN 37830 USA
| | - Yuanzhao Zhang
- Center for Applied Mathematics, Cornell University Ithaca NY 14583 USA
| | - Ruhong Zhou
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, Department of Physics, Zhejiang University Hangzhou 310027 China .,Department of Chemistry, Columbia University New York NY 10027 USA
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