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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Recent advances in computational methods for biosensor design. Biotechnol Bioeng 2020; 118:555-578. [PMID: 33135778 DOI: 10.1002/bit.27618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 01/20/2023]
Abstract
Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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Zhang Y, Ma Z, Wang Y, Boyer J, Ni G, Cheng L, Su S, Zhang Z, Zhu Z, Qian J, Su L, Zhang Q, Damania B, Liu P. Streptavidin Promotes DNA Binding and Activation of cGAS to Enhance Innate Immunity. iScience 2020; 23:101463. [PMID: 32861998 PMCID: PMC7476851 DOI: 10.1016/j.isci.2020.101463] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 06/15/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
cGAS/STING signaling plays an essential role in sensing cytosolic DNA. cGAS activity is regulated by posttranslational modifications and binding partners. cGAS interactome largely includes mammalian or viral proteins. Whether and how bacterial proteins bind cGAS to modulate innate immunity remain elusive. Here, we found streptavidin, a secreted bacterial protein, selectively bound cGAS to promote DNA-induced cGAS activation and interferon-β production. Mechanistically, streptavidin enhanced DNA binding and cGAS phase separation, therefore facilitating cGAS activation. Using an HSV-1-infected mouse model, we found streptavidin nanoparticles facilitated HSV-1 clearance through improving innate immunity. Considering the clinical usage of streptavidin as an immune stimulant and drug delivery vehicle and its biotechnological usage for biotin-labeled protein purification and detection, our studies not only provide an example for a bacterial protein regulating cGAS activity but also suggest caution needs to be taken when using streptavidin in various applications given to its ability to induce innate immunity.
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Affiliation(s)
- Yanqiong Zhang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhe Ma
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ying Wang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua Boyer
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Guoxin Ni
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Liang Cheng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Siyuan Su
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhigang Zhang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhichuan Zhu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jiayi Qian
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lishan Su
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Blossom Damania
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- University of North Carolina Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Poudel L, Twarock R, Steinmetz NF, Podgornik R, Ching WY. Impact of Hydrogen Bonding in the Binding Site between Capsid Protein and MS2 Bacteriophage ssRNA. J Phys Chem B 2017; 121:6321-6330. [PMID: 28581757 DOI: 10.1021/acs.jpcb.7b02569] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MS2 presents a well-studied example of a single-stranded RNA virus for which the genomic RNA plays a pivotal role in the virus assembly process based on the packaging signal-mediated mechanism. Packaging signals (PSs) are multiple dispersed RNA sequence/structure motifs varying around a central recognition motif that interact in a specific way with the capsid protein in the assembly process. Although the discovery and identification of these PSs was based on bioinformatics and geometric approaches, in tandem with sophisticated experimental protocols, we approach this problem using large-scale ab initio computation centered on critical aspects of the consensus protein-RNA interactions recognition motif. DFT calculations are carried out on two nucleoprotein complexes: wild-type and mutated (PDB IDs: 1ZDH and 5MSF ). The calculated partial charge distribution of residues and the strength of hydrogen bonding (HB) between them enabled us to locate the exact binding sites with the strongest HBs, identified to be LYS43-A-4, ARG49-C-13, TYR85-C-5, and LYS61-C-5, due to the change in the sequence of the mutated RNA.
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Affiliation(s)
- Lokendra Poudel
- Department of Physics and Astronomy, University of Missouri-Kansas City , Kansas City, Missouri 64110, United States
| | - Reidun Twarock
- Department of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York , York YO10 5DD, United Kingdom
| | | | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute , SI-1000 Ljubljana, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana , SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City , Kansas City, Missouri 64110, United States
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Andreoni A, Nardo L, Rigler R. Time-resolved homo-FRET studies of biotin-streptavidin complexes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:656-662. [PMID: 27494295 DOI: 10.1016/j.jphotobiol.2016.07.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 07/27/2016] [Indexed: 11/25/2022]
Abstract
Förster resonance energy transfer is a mechanism of fluorescence quenching that is notably useful for characterizing properties of biomolecules and/or their interactions. Here we study water-solutions of Biotin-Streptavidin complexes, in which Biotin is labeled with a rigidly-bound fluorophore that can interact by Förster resonance energy transfer with the fluorophores labeling the other, up to three, Biotins of the same complex. The fluorophore, Atto550, is a Rhodamine analogue. We detect the time-resolved fluorescence decay of the fluorophores with an apparatus endowed with single-photon sensitivity and temporal resolution of ~30ps. The decay profiles we observe for samples containing constant Biotin-Atto550 conjugates and varying Streptavidin concentrations are multi-exponential. Each decay component can be associated with the rate of quenching exerted on each donor by each of the acceptors that label the other Biotin molecules, depending on the binding site they occupy. The main features that lead to this result are that (i) the transition dipole moments of the up-to-four Atto550 fluorophores that label the complexes are fixed as to both relative positions and mutual orientations; (ii) the fluorophores are identical and the role of donor in each Biotin-Streptavidin complex is randomly attributed to the one that has absorbed the excitation light (homo-FRET). Obviously the high-temporal resolution of the excitation-detection apparatus is necessary to discriminate among the fluorescence decay components.
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Affiliation(s)
- Alessandra Andreoni
- Department of Science and High Technology, University of Insubria, Como 22100, Italy.
| | - Luca Nardo
- Department of Science and High Technology, University of Insubria, Como 22100, Italy.
| | - Rudolf Rigler
- Department of Medical Biophysics, Karolinska Institutet, 17 177 Stockholm, Sweden; Laboratory of Biomedical Optics, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland.
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Macchia E, Alberga D, Manoli K, Mangiatordi GF, Magliulo M, Palazzo G, Giordano F, Lattanzi G, Torsi L. Organic bioelectronics probing conformational changes in surface confined proteins. Sci Rep 2016; 6:28085. [PMID: 27312768 PMCID: PMC4911579 DOI: 10.1038/srep28085] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/31/2016] [Indexed: 02/07/2023] Open
Abstract
The study of proteins confined on a surface has attracted a great deal of attention due to its relevance in the development of bio-systems for laboratory and clinical settings. In this respect, organic bio-electronic platforms can be used as tools to achieve a deeper understanding of the processes involving protein interfaces. In this work, biotin-binding proteins have been integrated in two different organic thin-film transistor (TFT) configurations to separately address the changes occurring in the protein-ligand complex morphology and dipole moment. This has been achieved by decoupling the output current change upon binding, taken as the transducing signal, into its component figures of merit. In particular, the threshold voltage is related to the protein dipole moment, while the field-effect mobility is associated with conformational changes occurring in the proteins of the layer when ligand binding occurs. Molecular Dynamics simulations on the whole avidin tetramer in presence and absence of ligands were carried out, to evaluate how the tight interactions with the ligand affect the protein dipole moment and the conformation of the loops surrounding the binding pocket. These simulations allow assembling a rather complete picture of the studied interaction processes and support the interpretation of the experimental results.
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Affiliation(s)
- Eleonora Macchia
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Domenico Alberga
- Dipartimento Interateneo di Fisica "M. Merlin" dell'Università e del Politecnico di Bari - Bari (Italy)
| | - Kyriaki Manoli
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Giuseppe F Mangiatordi
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Maria Magliulo
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Gerardo Palazzo
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
| | - Francesco Giordano
- Dipartimento Interateneo di Fisica "M. Merlin" dell'Università e del Politecnico di Bari - Bari (Italy)
| | - Gianluca Lattanzi
- Dipartimento di Medicina Clinica e Sperimentale -Università degli Studi di Foggia - Foggia (Italy)
| | - Luisa Torsi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro - Bari (Italy)
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Liu F, Zhang JZH, Mei Y. The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations. Sci Rep 2016; 6:27190. [PMID: 27249234 PMCID: PMC4888747 DOI: 10.1038/srep27190] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/13/2016] [Indexed: 11/17/2022] Open
Abstract
Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.
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Affiliation(s)
- Fengjiao Liu
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - John Z. H. Zhang
- Department of Physics, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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Fraschetti C, Filippi A, Guarcini L, Steinmetz V, Speranza M. Structure and conformation of protonated D-(+)-biotin in the unsolvated state. J Phys Chem B 2015; 119:6198-203. [PMID: 25938640 DOI: 10.1021/acs.jpcb.5b02660] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A combined computational and infrared multiphoton dissociation (IRMPD) spectroscopic investigation shows that protonated d-(+)-biotin, formed in the gas phase by ESI-MS, acquires a folded structure with proton bonding between the ureido and valeryl carbonyls, and that only a single conformer of such a structure predominates. A uniform frequency vs distance correlation function is proposed for the O(+)-H···O and N-H···O bonds involved in the folded conformers of O2'-protonated d-(+)-biotin in the gas phase which, therefore, depends exclusively on the corresponding geometric parameters.
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Affiliation(s)
- Caterina Fraschetti
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università "La Sapienza", Roma, Italy
| | - Antonello Filippi
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università "La Sapienza", Roma, Italy
| | - Laura Guarcini
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università "La Sapienza", Roma, Italy
| | - Vincent Steinmetz
- ‡Laboratoire Chimie Physique, UMR8000 CNRS, Université Paris Sud 11, Orsay, France
| | - Maurizio Speranza
- †Dipartimento di Chimica e Tecnologie del Farmaco, Università "La Sapienza", Roma, Italy
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