1
|
Raza SHA, Zhong R, Yu X, Zhao G, Wei X, Lei H. Advances of Predicting Allosteric Mechanisms Through Protein Contact in New Technologies and Their Application. Mol Biotechnol 2023:10.1007/s12033-023-00951-4. [PMID: 37957479 DOI: 10.1007/s12033-023-00951-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023]
Abstract
Allostery is an intriguing phenomenon wherein the binding activity of a biological macromolecule is modulated via non-canonical binding site, resulting in synchronized functional changes. The mechanics underlying allostery are relatively complex and this review is focused on common methodologies used to study allostery, such as X-ray crystallography, NMR spectroscopy, and HDXMS. Different methodological approaches are used to generate data in different scenarios. For example, X-ray crystallography provides high-resolution structural information, NMR spectroscopy offers dynamic insights into allosteric interactions in solution, and HDXMS provides information on protein dynamics. The residue transition state (RTS) approach has emerged as a critical tool in understanding the energetics and conformational changes associated with allosteric regulation. Allostery has significant implications in drug discovery, gene transcription, disease diagnosis, and enzyme catalysis. Enzymes' catalytic activity can be modulated by allosteric regulation, offering opportunities to develop novel therapeutic alternatives. Understanding allosteric mechanisms associated with infectious organisms like SARS-CoV and bacterial pathogens can aid in the development of new antiviral drugs and antibiotics. Allosteric mechanisms are crucial in the regulation of a variety of signal transduction and cell metabolism pathways, which in turn govern various cellular processes. Despite progress, challenges remain in identifying allosteric sites and characterizing their contribution to a variety of biological processes. Increased understanding of these mechanisms can help develop allosteric systems specifically designed to modulate key biological mechanisms, providing novel opportunities for the development of targeted therapeutics. Therefore, the current review aims to summarize common methodologies that are used to further our understanding of allosteric mechanisms. In conclusion, this review provides insights into the methodologies used for the study of allostery, its applications in in silico modeling, the mechanisms underlying antibody allostery, and the ongoing challenges and prospects in advancing our comprehension of this intriguing phenomenon.
Collapse
Affiliation(s)
- Sayed Haidar Abbas Raza
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ruimin Zhong
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
| | - Xiaoting Yu
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Gang Zhao
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoqun Wei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- Licheng Detection and Certification Group Co., Ltd., Zhongshan, 528403, Guangdong, China.
| |
Collapse
|
2
|
Allert MJ, Kumar S, Wang Y, Beese LS, Hellinga HW. Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching. Commun Chem 2023; 6:168. [PMID: 37598249 PMCID: PMC10439942 DOI: 10.1038/s42004-023-00982-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023] Open
Abstract
Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.
Collapse
Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shivesh Kumar
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - You Wang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.
| |
Collapse
|
3
|
Protein Function Analysis through Machine Learning. Biomolecules 2022; 12:biom12091246. [PMID: 36139085 PMCID: PMC9496392 DOI: 10.3390/biom12091246] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein–ligand binding, including allosteric effects, protein–protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.
Collapse
|
4
|
Phillips JC, Moret MA, Zebende GF, Chow CC. Phase transitions may explain why SARS-CoV-2 spreads so fast and why new variants are spreading faster. PHYSICA A 2022; 598:127318. [PMID: 35431416 PMCID: PMC9004254 DOI: 10.1016/j.physa.2022.127318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 10/26/2021] [Indexed: 05/11/2023]
Abstract
The novel coronavirus SARS CoV-2 responsible for the COVID-19 pandemic and SARS CoV-1 responsible for the SARS epidemic of 2002-2003 share an ancestor yet evolved to have much different transmissibility and global impact 1. A previously developed thermodynamic model of protein conformations hypothesized that SARS CoV-2 is very close to a new thermodynamic critical point, which makes it highly infectious but also easily displaced by a spike-based vaccine because there is a tradeoff between transmissibility and robustness 2. The model identified a small cluster of four key mutations of SARS CoV-2 that predicts much stronger viral attachment and viral spreading compared to SARS CoV-1. Here we apply the model to the SARS-CoV-2 variants Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2)3 and predict, using no free parameters, how the new mutations will not diminish the effectiveness of current spike based vaccines and may even further enhance infectiousness by augmenting the binding ability of the virus.
Collapse
Affiliation(s)
- J C Phillips
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, United States of America
| | | | - Gilney F Zebende
- Department of Physics, State University of Feira de Santana, BA, Brazil
| | - Carson C Chow
- Mathematical Biology Section, NIDDK, NIH, Bethesda, Md 20892, United States of America
| |
Collapse
|
5
|
Zhou G, Lu X, Yuan M, Li T, Li L. Enzymatic Cycle-Inspired Dynamic Biosensors Affording No False-Positive Identification. Anal Chem 2021; 93:15482-15492. [PMID: 34767335 DOI: 10.1021/acs.analchem.1c03502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is an urgent need for reliable biosensors to detect nucleic acid of interest in clinical samples. We propose that the accuracy of the present nucleic acid-sensing method can be advanced by avoiding false-positive identifications derived from nonspecific interactions (e.g., nonspecific binding, probe degradation). The challenge is to exploit biosensors that can distinguish false-positive from true-positive samples in nucleic acid screening. In the present study, by learning from the enzymatic cycle in nature, we raise an allostery tool displaying invertible positive/negative cooperativity for reversible or cyclic activity control of the biosensing probe. We demonstrate that the silencing and regeneration of a positive (or negative) allosteric effector can be carried out through toehold displacement or an enzymatic reaction. We, thus, have developed several dynamic biosensors that can repeatedly measure a single nucleic acid sample. The ability to distinguish a false-positive from a true-positive signal is ascribed to the nonspecific interaction presenting equivalent signal variations, while the specific target binding exhibits diverse signal variations according to repeated measurements. Given its precise identification, such consequent dynamic biosensors offer exciting opportunities in physiological and pathological diagnosis.
Collapse
Affiliation(s)
- Guobao Zhou
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Xing Lu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Mengmeng Yuan
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Tuqiang Li
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Lei Li
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| |
Collapse
|
6
|
Periplasmic-binding protein-based biosensors and bioanalytical assay platforms: Advances, considerations, and strategies for optimal utility. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
7
|
Liu L, Yuan M, Jin Y, Zhou G, Li T, Li L, Peng H, Chen W. Tunable Dual-Effector Allostery System for Nucleic Acid Analysis with Enhanced Sensitivity and an Extended Dynamic Range. Anal Chem 2021; 93:8170-8177. [PMID: 34096261 DOI: 10.1021/acs.analchem.1c00055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the last few years, studies have demonstrated the existence of dual-effector allosteric cooperativity in nature and the mechanism underlying enhanced activation/inhibition performance. In this work, we design an artificial dual-effector allostery system for the construction of a dynamic biosensor that can achieve nucleic acid detection with superior sensitivity and across an extraordinary broad detection range. Our dual-effector allostery-regulated biosensor is based on the multibranched hybridization chain reaction (mHCR) involving three hairpins (H1, H2, and H3). In the presence of the target nucleic acid, the mHCR is initiated via cascading strand displacement events. The products of mHCR are then captured on the electrode surface based on the mechanism of the multivalent proximity ligation assay (mPLA) and the multivalent binding assay (mBA). The subsequent conjugation of streptavidin-modified horseradish peroxidase (SA-HRP) can lead to an increase in the electrochemical signal. Importantly, two distinct allosteric activation sites and two distinct allosteric inhibition sites in H1 are designed to fine-tune the nucleic acid detection sensitivity and the dynamic range. Using this new dual-effector allostery tool, we report the detection of nucleic acid at a dynamic range spanning 10-1012 aM, 11 orders of magnitude showing the broadest dynamic range reported to date with an allosteric regulation biosensor construct.
Collapse
Affiliation(s)
- Liangliang Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, P. R. China
| | - Mengmeng Yuan
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Yuxia Jin
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Guobao Zhou
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Tuqiang Li
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Lei Li
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Huaping Peng
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, P. R. China
| | - Wei Chen
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, P. R. China
| |
Collapse
|
8
|
Nakano S, Konishi H, Morii T. Receptor-based fluorescent sensors constructed from ribonucleopeptide. Methods Enzymol 2020; 641:183-223. [PMID: 32713523 DOI: 10.1016/bs.mie.2020.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Receptor-based fluorescent sensors are the representative tool for quantitative detection of target ligands. The high substrate-selectivity originated from biomacromolecule receptor is one of the advantages of this tool, but a laborious trial and error is usually required to construct sensors showing satisfactory fluorescence intensity changes without diminishing the function of parent receptor. Ribonucleopeptide (RNP) provides a scaffold of fluorescent sensors to improve such issues. RNP receptors for the ligand of interest are constructed by applying in vitro selection for RNA-derived RNP library. Simple modification of the N-terminal of peptide in RNP by an appropriate fluorophore converts the RNP receptor into the fluorescent sensor with retaining the affinity and selectivity for the substrate. In this chapter, we introduce the protocols for construction of fluorescent RNP sensors through selection from a library of fluorophore-modified RNP complex or by a structure-based modular design. Furthermore, we describe the application of covalently linked RNP sensors for simultaneous detection of multiple ligands.
Collapse
Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Hiroaki Konishi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
| |
Collapse
|
9
|
Snoek T, Chaberski EK, Ambri F, Kol S, Bjørn SP, Pang B, Barajas JF, Welner DH, Jensen MK, Keasling JD. Evolution-guided engineering of small-molecule biosensors. Nucleic Acids Res 2020; 48:e3. [PMID: 31777933 PMCID: PMC6943132 DOI: 10.1093/nar/gkz954] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/06/2019] [Accepted: 10/24/2019] [Indexed: 11/14/2022] Open
Abstract
Allosteric transcription factors (aTFs) have proven widely applicable for biotechnology and synthetic biology as ligand-specific biosensors enabling real-time monitoring, selection and regulation of cellular metabolism. However, both the biosensor specificity and the correlation between ligand concentration and biosensor output signal, also known as the transfer function, often needs to be optimized before meeting application needs. Here, we present a versatile and high-throughput method to evolve prokaryotic aTF specificity and transfer functions in a eukaryote chassis, namely baker's yeast Saccharomyces cerevisiae. From a single round of mutagenesis of the effector-binding domain (EBD) coupled with various toggled selection regimes, we robustly select aTF variants of the cis,cis-muconic acid-inducible transcription factor BenM evolved for change in ligand specificity, increased dynamic output range, shifts in operational range, and a complete inversion-of-function from activation to repression. Importantly, by targeting only the EBD, the evolved biosensors display DNA-binding affinities similar to BenM, and are functional when ported back into a prokaryotic chassis. The developed platform technology thus leverages aTF evolvability for the development of new host-agnostic biosensors with user-defined small-molecule specificities and transfer functions.
Collapse
Affiliation(s)
- Tim Snoek
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Evan K Chaberski
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sara P Bjørn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bo Pang
- Joint BioEnergy Institute, Emeryville, CA, USA
| | | | - Ditte H Welner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.,Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, USA.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| |
Collapse
|
10
|
A genetically encoded fluorescent sensor for in vivo imaging of GABA. Nat Methods 2019; 16:763-770. [DOI: 10.1038/s41592-019-0471-2] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/28/2019] [Indexed: 12/13/2022]
|
11
|
Ko W, Kumar R, Kim S, Lee HS. Construction of Bacterial Cells with an Active Transport System for Unnatural Amino Acids. ACS Synth Biol 2019; 8:1195-1203. [PMID: 30971082 DOI: 10.1021/acssynbio.9b00076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Engineered organisms with an expanded genetic code have attracted much attention in chemical and synthetic biology research. In this work, engineered bacterial organisms with enhanced unnatural amino acid (UAA) uptake abilities were developed by screening periplasmic binding protein (PBP) mutants for recognition of UAAs. A FRET-based assay was used to identify a mutant PBP (LBP-AEL) with excellent binding affinity ( Kd ≈ 500 nM) to multiple UAAs from 37 mutants. Bacterial cells expressing LBP-AEL showed up to 5-fold enhanced uptake of UAAs, which was determined by genetic incorporation of UAAs into a green fluorescent protein and measuring UAA concentration in cell lysates. To the best of our knowledge, this work is the first report of engineering cellular uptake of UAAs and could provide an impetus for designing advanced unnatural organisms with an expanded genetic code, which function with the efficiency comparable to that of natural organisms. The system would be useful to increase mutant protein yield from lower concentrations of UAAs for industrial and large-scale applications. In addition, the techniques used in this report such as the sensor design and the measurement of UAA concentration in cell lysates could be useful for other biochemical applications.
Collapse
Affiliation(s)
- Wooseok Ko
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Rahul Kumar
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Sanggil Kim
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| |
Collapse
|
12
|
Lu X, Zhou G, Zeng Y, Yin Z, Zhang Z, Guo L, Zhai Y, Yang Y, Wang H, Li L. Single-step multivalent capture assay for nucleic acid detection with dual-affinity regulation using mutation inhibition and allosteric activation. Chem Sci 2019; 10:5025-5030. [PMID: 31183052 PMCID: PMC6530536 DOI: 10.1039/c9sc01199d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 04/04/2019] [Indexed: 12/31/2022] Open
Abstract
A single-step electrocatalytic biosensor with dual-affinity regulation enables a tunable dynamic range and tunable single nucleotide resolution for nucleic acid detection.
The rational modulation of receptor affinity through distal-site mutation and allosteric control is valuable in biosensor designing to tune the useful dynamic range. Our ability to programmatically engineer dual-affinity regulation into diverse affinities of target binding and activities of hybridization chain reaction, however, remains limited. By programmable engineering of the switching equilibria of the recognition hairpin using distal-site mutation inhibition and allosteric activation, we obtained a set of receptors varying significantly in affinities of target binding and activities of the hybridization chain reaction. For the first time, we developed an electrocatalytic biosensor for nucleic acid detection with a tunable dynamic range based on a conformational switch triggered bidirectional hybridization chain reaction and blocker assisted multivalent binding. This designable biosensor thus enables single-step incubation, diverse affinities of target binding, diverse efficiencies of signal amplification and diverse single nucleotide discrimination for quantitative analyses of nucleic acids of various lengths in serum, which holds great potential as a compelling platform suitable for liquid biopsy.
Collapse
Affiliation(s)
- Xing Lu
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Guobao Zhou
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Yanbo Zeng
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Zhengzhi Yin
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Zulei Zhang
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Liping Guo
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Yunyun Zhai
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Yiwen Yang
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Hailong Wang
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| | - Lei Li
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , China . ;
| |
Collapse
|
13
|
Nakano S, Shimizu M, Dinh H, Morii T. Highly selective dual sensing of ATP and ADP using fluorescent ribonucleopeptide sensors. Chem Commun (Camb) 2019; 55:1611-1614. [PMID: 30657140 DOI: 10.1039/c8cc09934k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Highly selective fluorescent sensors for ATP and ADP were constructed from RNA aptamers by applying a modular design of a ribonucleopeptide scaffold. These sensors allow facile and quantitative detection of ATP and ADP simultaneously in a solution and enable monitoring of the time-course changes of ATP and ADP concentrations in an enzymatic reaction.
Collapse
Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
| | | | | | | |
Collapse
|
14
|
Mariottini D, Idili A, Nijenhuis MAD, de Greef TFA, Ricci F. DNA-Based Nanodevices Controlled by Purely Entropic Linker Domains. J Am Chem Soc 2018; 140:14725-14734. [PMID: 30351025 DOI: 10.1021/jacs.8b07640] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We demonstrate here the rational design of purely entropic domains as a versatile approach to achieve control of the input/output response of synthetic molecular receptors. To do so and to highlight the versatility and generality of this approach, we have rationally re-engineered two model DNA-based receptors: a clamp-like DNA-based switch that recognizes a specific DNA sequence and an ATP-binding aptamer. We show that, by varying the length of the linker domain that connects the two recognition portions of these receptors, it is possible to finely control their affinity for their specific ligand. Through mathematical modeling and thermodynamic characterization, we also demonstrate for both systems that entropy changes associated with changes in linker length are responsible for affinity modulation and that the linker we have designed behaves as a disordered random-coil polymer. The approach also allows us to regulate the ligand concentration range at which the receptors respond and show optimal specificity. Given these attributes, the use of purely entropic domains appears as a versatile and general approach to finely control the activity of synthetic receptors in a highly predictable and controlled fashion.
Collapse
Affiliation(s)
- Davide Mariottini
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , 00133 Rome , Italy
| | - Andrea Idili
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , 00133 Rome , Italy
| | - Minke A D Nijenhuis
- Institute for Complex Molecular Systems , Eindhoven University of Technology , 5600 MB Eindhoven , The Netherlands
| | - Tom F A de Greef
- Institute for Complex Molecular Systems , Eindhoven University of Technology , 5600 MB Eindhoven , The Netherlands
| | - Francesco Ricci
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , 00133 Rome , Italy
| |
Collapse
|
15
|
Field LD, Walper SA, Susumu K, Lasarte-Aragones G, Oh E, Medintz IL, Delehanty JB. A Quantum Dot-Protein Bioconjugate That Provides for Extracellular Control of Intracellular Drug Release. Bioconjug Chem 2018; 29:2455-2467. [DOI: 10.1021/acs.bioconjchem.8b00357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lauren D. Field
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- KeyW Corporation, Hanover, Maryland 21076, United States
| | - Guillermo Lasarte-Aragones
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- George Mason University, College of Sciences, Fairfax, Virginia 22030 United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- KeyW Corporation, Hanover, Maryland 21076, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - James B. Delehanty
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| |
Collapse
|
16
|
Teanphonkrang S, Janke S, Chaiyen P, Sucharitakul J, Suginta W, Khunkaewla P, Schuhmann W, Ruff A, Schulte A. Tuned Amperometric Detection of Reduced β-Nicotinamide Adenine Dinucleotide by Allosteric Modulation of the Reductase Component of the p-Hydroxyphenylacetate Hydroxylase Immobilized within a Redox Polymer. Anal Chem 2018; 90:5703-5711. [PMID: 29633834 DOI: 10.1021/acs.analchem.7b05467] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the fabrication of an amperometric NADH biosensor system that employs an allosterically modulated bacterial reductase in an adapted osmium(III)-complex-modified redox polymer film for analyte quantification. Chains of complexed Os(III) centers along matrix polymer strings make electrical connection between the immobilized redox protein and a graphite electrode disc, transducing enzymatic oxidation of NADH into a biosensor current. Sustainable anodic signaling required (1) a redox polymer with a formal potential that matched the redox switch of the embedded reductase and avoided interfering redox interactions and (2) formation of a cross-linked enzyme/polymer film for stable biocatalyst entrapment. The activity of the chosen reductase is enhanced upon binding of an effector, i.e. p-hydroxy-phenylacetic acid ( p-HPA), allowing the acceleration of the substrate conversion rate on the sensor surface by in situ addition or preincubation with p-HPA. Acceleration of NADH oxidation amplified the response of the biosensor, with a 1.5-fold increase in the sensitivity of analyte detection, compared to operation without the allosteric modulator. Repetitive quantitative testing of solutions of known NADH concentration verified the performance in terms of reliability and analyte recovery. We herewith established the use of allosteric enzyme modulation and redox polymer-based enzyme electrode wiring for substrate biosensing, a concept that may be applicable to other allosteric enzymes.
Collapse
Affiliation(s)
- Somjai Teanphonkrang
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Salome Janke
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry , Chulalongkorn University , 10330 Bangkok , Thailand
| | - Wipa Suginta
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand.,Center of Excellence (CoE) in Advanced Functional Materials, Institute of Science , Suranaree University of Technology , Nakhon Ratchasima 30000 , Thailand
| | - Panida Khunkaewla
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Wolfgang Schuhmann
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Adrian Ruff
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
| |
Collapse
|
17
|
Ko W, Kim S, Lee HS. Engineering a periplasmic binding protein for amino acid sensors with improved binding properties. Org Biomol Chem 2018; 15:8761-8769. [PMID: 28994436 DOI: 10.1039/c7ob02165h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Periplasmic binding proteins (PBPs) are members of a widely distributed protein superfamily found in bacteria and archaea, and are involved in the cellular uptake of solutes. In this report, a leucine-binding PBP was engineered to detect l-Leu based on a fluorescence resonance energy transfer (FRET) change upon ligand binding. A fluorescent unnatural amino acid, l-(7-hydroxycoumarin-4-yl)ethylglycine (CouA), was genetically incorporated into the protein as a FRET donor, and a yellow fluorescent protein (YFP) was fused with its N-terminus as a FRET acceptor. When CouA was incorporated into position 178, the sensor protein showed a 2.5-fold increase in the FRET ratio. Protein engineering significantly improved its substrate specificity, showing minimal changes in the FRET ratio with the other 19 natural amino acids and d-Leu. Further modification increased the sensitivity of the sensor protein (14-fold) towards l-Leu, and it recognized l-Met as well with moderate binding affinity. Selected mutant sensors were used to measure concentrations of l-Leu in a biological sample (fetal bovine serum) and to determine the optical purity of Leu and Met. This FRET-based sensor design strategy allowed us to easily manipulate the natural receptor to improve its binding affinity and specificity and to recognize other natural molecules, which are not recognized by the wild-type receptor. The design strategy can be applied to other natural receptors, enabling engineering receptors that sense biochemically interesting molecules.
Collapse
Affiliation(s)
- Wooseok Ko
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea.
| | | | | |
Collapse
|
18
|
Nakano S, Tamura T, Das RK, Nakata E, Chang YT, Morii T. A Diversity-Oriented Library of Fluorophore-Modified Receptors Constructed from a Chemical Library of Synthetic Fluorophores. Chembiochem 2017; 18:2212-2216. [PMID: 28879678 DOI: 10.1002/cbic.201700403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/16/2022]
Abstract
The practical application of biosensors can be determined by evaluating the sensing ability of fluorophore-modified derivatives of a receptor with appropriate recognition characteristics for target molecules. One of the key determinants for successfully obtaining a useful biosensor is wide variation in the fluorophores attached to a given receptor. Thus, using a larger fluorophore-modified receptor library provides a higher probability of obtaining a practically useful biosensor. However, no effective method has yet been developed for constructing such a diverse library of fluorophore-modified receptors. Herein, we report a method for constructing fluorophore-modified receptors by using a chemical library of synthetic fluorophores with a thiol-reactive group. This library was converted into a library of fluorophore-modified adenosine-binding ribonucleopeptide (RNP) receptors by introducing the fluorophores to the Rev peptide of the RNP complex by alkylation of the thiol group. This method enabled the construction of 263 fluorophore-modified ATP-binding RNP receptors and allowed the selection of suitable receptor-based fluorescent sensors that target ATP.
Collapse
Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Raj Kumar Das
- Bharat Petroleum Corporation Ltd., Corporate R&D Centre, Plot No. 2 A, Udyog Kendra, Surajpur Industrial Area, Greater Noida, 201 306, India
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Young-Tae Chang
- Department of Chemistry and MedChem Program of Life Sciences, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| |
Collapse
|
19
|
Nikolić D, Kovačev-Nikolić V. Dynamical persistence of active sites identified in maltose-binding protein. J Mol Model 2017; 23:167. [PMID: 28451879 DOI: 10.1007/s00894-017-3344-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
Abstract
This study identifies dynamical properties of maltose-binding protein (MBP) useful in unveiling active site residues susceptible to ligand binding. The described methodology has been previously used in support of novel topological techniques of persistent homology and statistical inference in complex, multi-scale, high-dimensional data often encountered in computational biophysics. Here we outline a computational protocol that is based on the anisotropic elastic network models of 14 all-atom three-dimensional protein structures. We introduce the notion of dynamical distance matrices as a measure of correlated interactions among 370 amino acid residues that constitute a single protein. The dynamical distance matrices serve as an input for a persistent homology suite of codes to further distinguish a small subset of residues with high affinity for ligand binding and allosteric activity. In addition, we show that ligand-free closed MBP structures require lower deformation energies than open MBP structures, which may be used in categorization of time-evolving molecular dynamics structures. Analysis of the most probable allosteric coupling pathways between active site residues and the protein exterior is also presented.
Collapse
Affiliation(s)
- Dragan Nikolić
- Department of Mechanical Engineering, University of Alberta and National Institute for Nanotechnology, 11421 Saskatchewan Dr NW, Edmonton, AB, T6G 2M9, Canada.
| | | |
Collapse
|
20
|
Younger AKD, Dalvie NC, Rottinghaus AG, Leonard JN. Engineering Modular Biosensors to Confer Metabolite-Responsive Regulation of Transcription. ACS Synth Biol 2017; 6:311-325. [PMID: 27744683 DOI: 10.1021/acssynbio.6b00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Efforts to engineer microbial factories have benefitted from mining biological diversity and high throughput synthesis of novel enzymatic pathways, yet screening and optimizing metabolic pathways remain rate-limiting steps. Metabolite-responsive biosensors may help to address these persistent challenges by enabling the monitoring of metabolite levels in individual cells and metabolite-responsive feedback control. We are currently limited to naturally evolved biosensors, which are insufficient for monitoring many metabolites of interest. Thus, a method for engineering novel biosensors would be powerful, yet we lack a generalizable approach that enables the construction of a wide range of biosensors. As a step toward this goal, we here explore several strategies for converting a metabolite-binding protein into a metabolite-responsive transcriptional regulator. By pairing a modular protein design approach with a library of synthetic promoters and applying robust statistical analyses, we identified strategies for engineering biosensor-regulated bacterial promoters and for achieving design-driven improvements of biosensor performance. We demonstrated the feasibility of this strategy by fusing a programmable DNA binding motif (zinc finger module) with a model ligand binding protein (maltose binding protein), to generate a novel biosensor conferring maltose-regulated gene expression. This systematic investigation provides insights that may guide the development of additional novel biosensors for diverse synthetic biology applications.
Collapse
Affiliation(s)
- Andrew K. D. Younger
- Interdisciplinary
Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil C. Dalvie
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Austin G. Rottinghaus
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Joshua N. Leonard
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert
H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
21
|
Conformational Change of a Tryptophan Residue in BtuF Facilitates Binding and Transport of Cobinamide by the Vitamin B12 Transporter BtuCD-F. Sci Rep 2017; 7:41575. [PMID: 28128319 PMCID: PMC5269720 DOI: 10.1038/srep41575] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/20/2016] [Indexed: 01/26/2023] Open
Abstract
BtuCD-F is an ABC transporter that mediates cobalamin uptake into Escherichia coli. Early in vivo data suggested that BtuCD-F might also be involved in the uptake of cobinamide, a cobalamin precursor. However, neither was it demonstrated that BtuCD-F indeed transports cobinamide, nor was the structural basis of its recognition known. We synthesized radiolabeled cyano-cobinamide and demonstrated BtuCD-catalyzed in vitro transport, which was ATP- and BtuF-dependent. The crystal structure of cobinamide-bound BtuF revealed a conformational change of a tryptophan residue (W66) in the substrate binding cleft compared to the structure of cobalamin-bound BtuF. High-affinity binding of cobinamide was dependent on W66, because mutation to most other amino acids substantially reduced binding. The structures of three BtuF W66 mutants revealed that tight packing against bound cobinamide was only provided by tryptophan and phenylalanine, in line with the observed binding affinities. In vitro transport rates of cobinamide and cobalamin were not influenced by the substitutions of BtuF W66 under the experimental conditions, indicating that W66 has no critical role in the transport reaction. Our data present the molecular basis of the cobinamide versus cobalamin specificity of BtuCD-F and provide tools for in vitro cobinamide transport and binding assays.
Collapse
|
22
|
Kovacev-Nikolic V, Bubenik P, Nikolić D, Heo G. Using persistent homology and dynamical distances to analyze protein binding. Stat Appl Genet Mol Biol 2016; 15:19-38. [PMID: 26812805 DOI: 10.1515/sagmb-2015-0057] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic, the persistence landscape, was recently introduced by Bubenik. It is a functional summary, so it is easy to calculate sample means and variances, and it is straightforward to construct various test statistics. Implementing a permutation test we detect conformational changes between closed and open forms of the maltose-binding protein, a large biomolecule consisting of 370 amino acid residues. Furthermore, persistence landscapes can be applied to machine learning methods. A hyperplane from a support vector machine shows the clear separation between the closed and open proteins conformations. Moreover, because our approach captures dynamical properties of the protein our results may help in identifying residues susceptible to ligand binding; we show that the majority of active site residues and allosteric pathway residues are located in the vicinity of the most persistent loop in the corresponding filtered Vietoris-Rips complex. This finding was not observed in the classical anisotropic network model.
Collapse
|
23
|
Mitchell JA, Whitfield JH, Zhang WH, Henneberger C, Janovjak H, O’Mara ML, Jackson CJ. Rangefinder: A Semisynthetic FRET Sensor Design Algorithm. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua A. Mitchell
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Jason H. Whitfield
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - William H. Zhang
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Christian Henneberger
- Institute
of Neurology, University College London, London, WC1E 6BT, United Kingdom
- German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
- Institute
of Cellular Neurosciences, University of Bonn, 53113 Bonn, Germany
| | - Harald Janovjak
- Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Megan L. O’Mara
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| |
Collapse
|
24
|
Lv D, Li C, Tan J, Zhang X, Wang C, Su J. Identification of functionally key residues in maltose transporter with an elastic network model-based thermodynamic method. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1234077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Dashuai Lv
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Chunhua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Jianjun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Xiaoyi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Cunxin Wang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Jiguo Su
- College of Science, Yanshan University, Qinhuangdao, China
| |
Collapse
|
25
|
Song P, Li M, Shen J, Pei H, Chao J, Su S, Aldalbahi A, Wang L, Shi J, Song S, Wang L, Fan C, Zuo X. Dynamic Modulation of DNA Hybridization Using Allosteric DNA Tetrahedral Nanostructures. Anal Chem 2016; 88:8043-9. [DOI: 10.1021/acs.analchem.6b01373] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ping Song
- Division
of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation
Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Min Li
- Division
of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation
Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Juwen Shen
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Hao Pei
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Jie Chao
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM) and School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Shao Su
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM) and School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Ali Aldalbahi
- Chemistry
Department, King Saud University, Riyadh 11451, Saudi Arabia
| | - Lihua Wang
- Division
of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation
Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- Kellogg
College, University of Oxford, Oxford, OX2 6PN, United Kingdom
| | - Shiping Song
- Division
of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation
Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lianhui Wang
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM) and School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Chunhai Fan
- Division
of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation
Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaolei Zuo
- Division
of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation
Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| |
Collapse
|
26
|
Hasmoni SH, Mau GK, Karsani SA, Cass A, Shahir S. Strep-tag II Mutant Maltose-binding Protein for Reagentless Fluorescence Sensing. Trop Life Sci Res 2016; 27:63-75. [PMID: 27019682 PMCID: PMC4807963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
Maltose-binding protein (MBP) is a periplasmic binding protein found in Gram negative bacteria. MBP is involved in maltose transport and bacterial chemotaxis; it binds to maltose and maltodextrins comprising α(1-4)-glucosidically linked linear glucose polymers and α(1-4)-glucosidically linked cyclodextrins. Upon ligand binding, MBP changes its conformation from an open to a closed form. This molecular recognition-transducing a ligand-binding event into a physical one-renders MBP an ideal candidate for biosensor development. Here, we describe the construction of a Strep-tag II mutant MBP for reagentless fluorescence sensing. malE, which encodes MBP, was amplified. A cysteine residue was introduced by site-directed mutagenesis to ensure a single label attachment at a specific site with a thiol-specific fluorescent probe. An environmentally sensitive fluorophore (IANBD amide) was covalently attached to the introduced thiol group and analysed by fluorescence sensing. The tagged mutant MBP (D95C) was purified (molecular size, ∼42 kDa). The fluorescence measurements of the IANBD-labelled Strep-tag II-D95C in the solution phase showed an appreciable change in fluorescence intensity (dissociation constant, 7.6±1.75 μM). Our mutant MBP retains maltose-binding activity and is suitable for reagentless fluorescence sensing.
Collapse
Affiliation(s)
- Siti Halimah Hasmoni
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Goh Kian Mau
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Saiful Anuar Karsani
- Department of Biochemistry, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Anthony Cass
- Department of Chemistry and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Shafinaz Shahir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| |
Collapse
|
27
|
Monomeric Corynebacterium glutamicum N-acetyl glutamate kinase maintains sensitivity to L-arginine but has a lower intrinsic catalytic activity. Appl Microbiol Biotechnol 2015; 100:1789-1798. [DOI: 10.1007/s00253-015-7065-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 09/29/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
|
28
|
Lipska AG, Sieradzan AK, Krupa P, Mozolewska MA, D’Auria S, Liwo A. Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field. J Mol Model 2015; 21:64. [DOI: 10.1007/s00894-015-2609-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/08/2015] [Indexed: 11/30/2022]
|
29
|
Lundin D, Berggren G, Logan DT, Sjöberg BM. The origin and evolution of ribonucleotide reduction. Life (Basel) 2015; 5:604-36. [PMID: 25734234 PMCID: PMC4390871 DOI: 10.3390/life5010604] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs.
Collapse
Affiliation(s)
- Daniel Lundin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Gustav Berggren
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| |
Collapse
|
30
|
Ozyurt C, Evran S, Telefoncu A. Development of genetically encoded fluorescent protein constructs of hyperthermophilic maltose-binding protein. Prep Biochem Biotechnol 2014; 44:132-45. [PMID: 24152100 DOI: 10.1080/10826068.2013.797436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Circularly permuted green fluorescent protein (cGFP) was inserted into the hyperthermophilic maltose binding protein at two different locations. cGFP was inserted between amino acid residues 206 and 207, or fused to the N-terminal of maltose binding protein from Thermotoga maritima. The cloned DNA constructs were expressed in Escherichia coli cells, and purified by metal chelate affinity chromatography. Conformational change upon ligand binding was monitored by the increase in fluorescence intensity. Both of the fusion proteins developed significant fluorescence change at 0.5 mM maltose concentration, whereas their maltose binding affinities and optimum incubation times were different. Fluorescent biosensors based on mesophilic maltose binding proteins have been described in the literature, but there is a growing interest in biosensors based on thermostable proteins. Therefore, the developed protein constructs could be models for thermophilic protein-based fluorescent biosensors.
Collapse
Affiliation(s)
- Canan Ozyurt
- a Department of Biochemistry, Faculty of Science , Ege University , Izmir , Turkey
| | | | | |
Collapse
|
31
|
Deacon LJ, Billones H, Galyean AA, Donaldson T, Pennacchio A, Iozzino L, D'Auria S, Dattelbaum JD. Tryptophan-scanning mutagenesis of the ligand binding pocket in Thermotoga maritima arginine-binding protein. Biochimie 2013; 99:208-14. [PMID: 24370478 DOI: 10.1016/j.biochi.2013.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 12/11/2013] [Indexed: 11/28/2022]
Abstract
The Thermotoga maritima arginine binding protein (TmArgBP) is a member of the periplasmic binding protein superfamily. As a highly thermostable protein, TmArgBP has been investigated for the potential to serve as a protein scaffold for the development of fluorescent protein biosensors. To establish a relationship between structural dynamics and ligand binding capabilities, we constructed single tryptophan mutants to probe the arginine binding pocket. Trp residues placed around the binding pocket reveal a strong dependence on fluorescence emission of the protein with arginine for all but one of the mutants. Using these data, we calculated dissociation constants of 1.9-3.3 μM for arginine. Stern-Volmer quenching analysis demonstrated that the protein undergoes a large conformational change upon ligand binding, which is a common feature of this protein superfamily. While still active at room temperature, time-resolved intensity and anisotropy decay data suggest that the protein exists as a highly rigid structure under these conditions. Interestingly, TmArgBP exists as a dimer at room temperature in both the presence and absence of arginine, as determined by asymmetric flow field flow fractionation (AF4) and supported by native gel-electrophoresis and time-resolved anisotropy. Our data on dynamics and stability will contribute to our understanding of hyperthermophilic proteins and their potential biotechnological applications.
Collapse
Affiliation(s)
- Lindsay J Deacon
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Hilbert Billones
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Anne A Galyean
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Teraya Donaldson
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Anna Pennacchio
- Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Luisa Iozzino
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA; Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Sabato D'Auria
- Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | | |
Collapse
|
32
|
Visualization of synaptic inhibition with an optogenetic sensor developed by cell-free protein engineering automation. J Neurosci 2013; 33:16297-309. [PMID: 24107961 DOI: 10.1523/jneurosci.4616-11.2013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We describe an engineered fluorescent optogenetic sensor, SuperClomeleon, that robustly detects inhibitory synaptic activity in single, cultured mouse neurons by reporting intracellular chloride changes produced by exogenous GABA or inhibitory synaptic activity. Using a cell-free protein engineering automation methodology that bypasses gene cloning, we iteratively constructed, produced, and assayed hundreds of mutations in binding-site residues to identify improvements in Clomeleon, a first-generation, suboptimal sensor. Structural analysis revealed that these improvements involve halide contacts and distant side chain rearrangements. The development of optogenetic sensors that respond to neural activity enables cellular tracking of neural activity using optical, rather than electrophysiological, signals. Construction of such sensors using in vitro protein engineering establishes a powerful approach for developing new probes for brain imaging.
Collapse
|
33
|
Siontorou CG, Batzias FA. A methodological combined framework for roadmapping biosensor research: a fault tree analysis approach within a strategic technology evaluation frame. Crit Rev Biotechnol 2013; 34:31-55. [PMID: 23919240 DOI: 10.3109/07388551.2013.790339] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Biosensor technology began in the 1960s to revolutionize instrumentation and measurement. Despite the glucose sensor market success that revolutionized medical diagnostics, and artificial pancreas promise currently the approval stage, the industry is reluctant to capitalize on other relevant university-produced knowledge and innovation. On the other hand, the scientific literature is extensive and persisting, while the number of university-hosted biosensor groups is growing. Considering the limited marketability of biosensors compared to the available research output, the biosensor field has been used by the present authors as a suitable paradigm for developing a methodological combined framework for "roadmapping" university research output in this discipline. This framework adopts the basic principles of the Analytic Hierarchy Process (AHP), replacing the lower level of technology alternatives with internal barriers (drawbacks, limitations, disadvantages), modeled through fault tree analysis (FTA) relying on fuzzy reasoning to count for uncertainty. The proposed methodology is validated retrospectively using ion selective field effect transistor (ISFET) - based biosensors as a case example, and then implemented prospectively membrane biosensors, putting an emphasis on the manufacturability issues. The analysis performed the trajectory of membrane platforms differently than the available market roadmaps that, considering the vast industrial experience in tailoring and handling crystallic forms, suggest the technology path of biomimetic and synthetic materials. The results presented herein indicate that future trajectories lie along with nanotechnology, and especially nanofabrication and nano-bioinformatics, and focused, more on the science-path, that is, on controlling the natural process of self-assembly and the thermodynamics of bioelement-lipid interaction. This retained the nature-derived sensitivity of the biosensor platform, pointing out the differences between the scope of academic research and the market viewpoint.
Collapse
Affiliation(s)
- Christina G Siontorou
- Department of Industrial Management and Technology, University of Piraeus , Karaoli and Dimitriou, Piraeus , Greece
| | | |
Collapse
|
34
|
Mcm10 self-association is mediated by an N-terminal coiled-coil domain. PLoS One 2013; 8:e70518. [PMID: 23894664 PMCID: PMC3720919 DOI: 10.1371/journal.pone.0070518] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/11/2013] [Indexed: 01/13/2023] Open
Abstract
Minichromosome maintenance protein 10 (Mcm10) is an essential eukaryotic DNA-binding replication factor thought to serve as a scaffold to coordinate enzymatic activities within the replisome. Mcm10 appears to function as an oligomer rather than in its monomeric form (or rather than as a monomer). However, various orthologs have been found to contain 1, 2, 3, 4, or 6 subunits and thus, this issue has remained controversial. Here, we show that self-association of Xenopus laevis Mcm10 is mediated by a conserved coiled-coil (CC) motif within the N-terminal domain (NTD). Crystallographic analysis of the CC at 2.4 Å resolution revealed a three-helix bundle, consistent with the formation of both dimeric and trimeric Mcm10 CCs in solution. Mutation of the side chains at the subunit interface disrupted in vitro dimerization of both the CC and the NTD as monitored by analytical ultracentrifugation. In addition, the same mutations also impeded self-interaction of the full-length protein in vivo, as measured by yeast-two hybrid assays. We conclude that Mcm10 likely forms dimers or trimers to promote its diverse functions during DNA replication.
Collapse
|
35
|
Takaoka Y, Ojida A, Hamachi I. Organische Proteinchemie und ihre Anwendung für Markierungen und Engineering in Lebendzellsystemen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207089] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
36
|
Takaoka Y, Ojida A, Hamachi I. Protein organic chemistry and applications for labeling and engineering in live-cell systems. Angew Chem Int Ed Engl 2013; 52:4088-106. [PMID: 23426903 DOI: 10.1002/anie.201207089] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Indexed: 12/11/2022]
Abstract
The modification of proteins with synthetic probes is a powerful means of elucidating and engineering the functions of proteins both in vitro and in live cells or in vivo. Herein we review recent progress in chemistry-based protein modification methods and their application in protein engineering, with particular emphasis on the following four strategies: 1) the bioconjugation reactions of amino acids on the surfaces of natural proteins, mainly applied in test-tube settings; 2) the bioorthogonal reactions of proteins with non-natural functional groups; 3) the coupling of recognition and reactive sites using an enzyme or short peptide tag-probe pair for labeling natural amino acids; and 4) ligand-directed labeling chemistries for the selective labeling of endogenous proteins in living systems. Overall, these techniques represent a useful set of tools for application in chemical biology, with the methods 2-4 in particular being applicable to crude (living) habitats. Although still in its infancy, the use of organic chemistry for the manipulation of endogenous proteins, with subsequent applications in living systems, represents a worthy challenge for many chemists.
Collapse
Affiliation(s)
- Yousuke Takaoka
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | | | | |
Collapse
|
37
|
Privman V, Zavalov O, Simonian A. Extended Linear Response for Bioanalytical Applications Using Multiple Enzymes. Anal Chem 2013; 85:2027-31. [DOI: 10.1021/ac302998y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, New York 13699, United
States
| | - Oleksandr Zavalov
- Department of Physics, Clarkson University, Potsdam, New York 13699, United
States
| | - Aleksandr Simonian
- Materials Research
and Education
Center, Auburn University, Auburn, Alabama
36849, United States
| |
Collapse
|
38
|
Impact of mutations on the allosteric conformational equilibrium. J Mol Biol 2012; 425:647-61. [PMID: 23228330 DOI: 10.1016/j.jmb.2012.11.041] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/27/2012] [Accepted: 11/30/2012] [Indexed: 11/21/2022]
Abstract
Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and effector-unbound protein structures. These simulations can be performed using our web server (http://salilab.org/allosmod/). We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a data set of 10 proteins and 179 mutations, we predict both the magnitude and the sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1k(B)T. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction.
Collapse
|
39
|
Structure-based model of allostery predicts coupling between distant sites. Proc Natl Acad Sci U S A 2012; 109:4875-80. [PMID: 22403063 DOI: 10.1073/pnas.1116274109] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Allostery is a phenomenon that couples effector ligand binding at an allosteric site to a structural and/or dynamic change at a distant regulated site. To study an allosteric transition, we vary the size of the allosteric site and its interactions to construct a series of energy landscapes with pronounced minima corresponding to both the effector bound and unbound crystal structures. We use molecular dynamics to sample these landscapes. The degree of perturbation by the effector, modeled by the size of the allosteric site, provides an order parameter for allostery that allows us to determine how microscopic motions give rise to commonly discussed macroscopic mechanisms: (i) induced fit, (ii) population shift, and (iii) entropy driven. These mechanisms involve decreasing structural differences between the effector bound and unbound populations. A metric (ligand-induced cooperativity) can measure how cooperatively a given regulated site responds to effector binding and therefore what kind of allosteric mechanism is involved. We apply the model to three proteins with experimentally characterized transitions: (i) calmodulin-GFP Ca(2+) sensor protein, (ii) maltose binding protein, and (iii) CSL transcription factor. Remarkably, the model is able to reproduce allosteric motion and predict coupling in a manner consistent with experiment.
Collapse
|
40
|
Vallée-Bélisle A, Ricci F, Plaxco KW. Engineering biosensors with extended, narrowed, or arbitrarily edited dynamic range. J Am Chem Soc 2012; 134:2876-9. [PMID: 22239688 DOI: 10.1021/ja209850j] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biomolecular recognition has long been an important theme in artificial sensing technologies. A current limitation of protein- and nucleic acid-based recognition, however, is that the useful dynamic range of single-site binding typically spans an 81-fold change in target concentration, an effect that limits the utility of biosensors in applications calling for either great sensitivity (a steeper relationship between target concentration and output signal) or the quantification of more wide-ranging concentrations. In response, we have adapted strategies employed by nature to modulate the input-output response of its biorecognition systems to rationally edit the useful dynamic range of an artificial biosensor. By engineering a structure-switching mechanism to tune the affinity of a receptor molecule, we first generated a set of receptor variants displaying similar specificities but different target affinities. Using combinations of these receptor variants (signaling and nonsignaling), we then rationally extended (to 900000-fold), narrowed (to 5-fold), and edited (three-state) the normally 81-fold dynamic range of a representative biosensor. We believe that these strategies may be widely applicable to technologies reliant on biorecognition.
Collapse
Affiliation(s)
- Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | | | | |
Collapse
|
41
|
Ruggiero A, Dattelbaum JD, Pennacchio A, Iozzino L, Staiano M, Luchansky MS, Der BS, Berisio R, D'Auria S, Vitagliano L. Crystallization and preliminary X-ray crystallographic analysis of ligand-free and arginine-bound forms of Thermotoga maritima arginine-binding protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1462-5. [PMID: 22102257 DOI: 10.1107/s1744309111037341] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 09/13/2011] [Indexed: 11/10/2022]
Abstract
The arginine-binding protein from Thermotoga maritima (TmArgBP) is an arginine-binding component of the ATP-binding cassette (ABC) transport system in this hyperthermophilic bacterium. This protein is endowed with an extraordinary stability towards thermal and chemical denaturation. Its structural characterization may provide useful insights for the clarification of structure-stability relationships and for the design of new biosensors. Crystallization trials were set up for both arginine-bound and ligand-free forms of TmArgBP and crystals suitable for crystallographic investigations were obtained for both forms. Ordered crystals of the arginine adduct of TmArgBP could only be obtained by using the detergent LDAO as an additive to the crystallization medium. These crystals were hexagonal, with unit-cell parameters a = 78.2, c = 434.7 Å, and diffracted to 2.7 Å resolution. The crystals of the ligand-free form were orthorhombic, with unit-cell parameters a = 51.8, b = 91.9, c = 117.9 Å, and diffracted to 2.25 Å resolution.
Collapse
Affiliation(s)
- Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Naples, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Gredell JA, Frei CS, Cirino PC. Protein and RNA engineering to customize microbial molecular reporting. Biotechnol J 2011; 7:477-99. [PMID: 22031507 DOI: 10.1002/biot.201100266] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/20/2011] [Accepted: 08/23/2011] [Indexed: 12/19/2022]
Abstract
Nature takes advantage of the malleability of protein and RNA sequence and structure to employ these macromolecules as molecular reporters whose conformation and functional roles depend on the presence of a specific ligand (an "effector" molecule). By following nature's example, ligand-responsive proteins and RNA molecules are now routinely engineered and incorporated into customized molecular reporting systems (biosensors). Microbial small-molecule biosensors and endogenous molecular reporters based on these sensing components find a variety of applications that include high-throughput screening of biosynthesis libraries, environmental monitoring, and novel gene regulation in synthetic biology. Here, we review recent advances in engineering small-molecule recognition by proteins and RNA and in coupling in vivo ligand binding to reporter-gene expression or to allosteric activation of a protein conferring a detectable phenotype. Emphasis is placed on microbial screening systems that serve as molecular reporters and facilitate engineering the ligand-binding component to recognize new molecules.
Collapse
Affiliation(s)
- Joseph A Gredell
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | | | | |
Collapse
|
43
|
Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins. Nat Struct Mol Biol 2011; 18:437-42. [PMID: 21378967 PMCID: PMC3077571 DOI: 10.1038/nsmb.2002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 12/07/2010] [Indexed: 01/06/2023]
Abstract
We describe a phage display methodology for engineering synthetic antigen binders (sABs) that recognize either the apo or the ligand-bound conformation of maltose-binding protein (MBP). sABs that preferentially recognize the maltose-bound form of MBP act as positive allosteric effectors by substantially increasing the affinity for maltose. A crystal structure of a sAB bound to the closed form of MBP reveals the basis for this allosteric effect. We show that sABs that recognize the bound form of MBP can rescue the function of a binding-deficient mutant by restoring its natural affinity for maltose. Furthermore, the sABs can enhance maltose binding in vivo, as they provide a growth advantage to bacteria under low-maltose conditions. The results demonstrate that structure-specific sABs can be engineered to dynamically control ligand-binding affinities by modulating the transition between different conformations.
Collapse
|
44
|
Takaoka Y, Sun Y, Tsukiji S, Hamachi I. Mechanisms of chemical protein19F-labeling and NMR-based biosensor construction in vitro and in cells using self-assembling ligand-directed tosylate compounds. Chem Sci 2011. [DOI: 10.1039/c0sc00513d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
45
|
Vallée-Bélisle A, Plaxco KW. Structure-switching biosensors: inspired by Nature. Curr Opin Struct Biol 2010; 20:518-26. [PMID: 20627702 DOI: 10.1016/j.sbi.2010.05.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/03/2010] [Accepted: 05/04/2010] [Indexed: 01/30/2023]
Abstract
Chemosensing in nature relies on biomolecular switches, biomolecules that undergo binding-induced changes in conformation or oligomerization to transduce chemical information into specific biochemical outputs. Motivated by the impressive performance of these natural 'biosensors,' which support continuous, real-time detection in highly complex environments, significant efforts have gone into the adaptation of such switches into artificial chemical sensors. Ongoing advances in the fields of protein and nucleic acid engineering (e.g. computational protein design, directed evolution, selection strategies and labeling chemistries) have greatly enhanced our ability to design new structure-switching sensors. Coupled with the development of advanced optical readout mechanisms, including genetically encoded fluorophores, and electrochemical readouts supporting detection directly in highly complex sample matrices, switch-based sensors have already seen deployment in applications ranging from real time, in vivo imaging to the continuous monitoring of drugs in blood serum.
Collapse
Affiliation(s)
- Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
46
|
A peptide-based fluorescent ratiometric sensor for quantitative detection of proteins. Anal Biochem 2010; 401:188-95. [PMID: 20188691 DOI: 10.1016/j.ab.2010.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 11/21/2022]
|
47
|
Environmentally sensitive fluorescent sensors based on synthetic peptides. SENSORS 2010; 10:3126-44. [PMID: 22319290 PMCID: PMC3274215 DOI: 10.3390/s100403126] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 02/27/2010] [Accepted: 03/24/2010] [Indexed: 01/02/2023]
Abstract
Biosensors allow the direct detection of molecular analytes, by associating a biological receptor with a transducer able to convert the analyte-receptor recognition event into a measurable signal. We review recent work aimed at developing synthetic fluorescent molecular sensors for a variety of analytes, based on peptidic receptors labeled with environmentally sensitive fluorophores. Fluorescent indicators based on synthetic peptides are highly interesting alternatives to protein-based sensors, since they can be synthesized chemically, are stable, and can be easily modified in a site-specific manner for fluorophore coupling and for immobilization on solid supports.
Collapse
|
48
|
Scirè A, Marabotti A, Staiano M, Iozzino L, Luchansky MS, Der BS, Dattelbaum JD, Tanfani F, D'Auria S. Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability. MOLECULAR BIOSYSTEMS 2010; 6:687-98. [PMID: 20237647 DOI: 10.1039/b922092e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
ABC transport systems provide selective passage of metabolites across cell membranes and typically require the presence of a soluble binding protein with high specificity to a specific ligand. In addition to their primary role in nutrient gathering, the binding proteins associated with bacterial transport systems have been studied for their potential to serve as design scaffolds for the development of fluorescent protein biosensors. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the physicochemical properties of a hyperthermophilic binding protein from Thermotoga maritima. We demonstrated preferential binding for the polar amino acid arginine and experimentally monitored the significant stabilization achieved upon binding of ligand to protein. The effect of temperature, pH, and detergent was also studied to provide a more complete picture of the protein dynamics. A protein structure model was obtained and molecular dynamic experiments were performed to investigate and couple the spectroscopic observations with specific secondary structural elements. The data determined the presence of a buried beta-sheet providing significant stability to the protein under all conditions investigated. The specific amino acid residues responsible for arginine binding were also identified. Our data on dynamics and stability will contribute to our understanding of bacterial binding protein family members and their potential biotechnological applications.
Collapse
Affiliation(s)
- Andrea Scirè
- Department of Biochemistry, Biology, and Genetics, Università Politecnica delle Marche, Ancona, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Design strategies of fluorescent biosensors based on biological macromolecular receptors. SENSORS 2010; 10:1355-76. [PMID: 22205872 PMCID: PMC3244018 DOI: 10.3390/s100201355] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 01/29/2010] [Accepted: 02/04/2010] [Indexed: 11/17/2022]
Abstract
Fluorescent biosensors to detect the bona fide events of biologically important molecules in living cells are increasingly demanded in the field of molecular cell biology. Recent advances in the development of fluorescent biosensors have made an outstanding contribution to elucidating not only the roles of individual biomolecules, but also the dynamic intracellular relationships between these molecules. However, rational design strategies of fluorescent biosensors are not as mature as they look. An insatiable request for the establishment of a more universal and versatile strategy continues to provide an attractive alternative, so-called modular strategy, which permits facile preparation of biosensors with tailored characteristics by a simple combination of a receptor and a signal transducer. This review describes an overview of the progress in design strategies of fluorescent biosensors, such as auto-fluorescent protein-based biosensors, protein-based biosensors covalently modified with synthetic fluorophores, and signaling aptamers, and highlights the insight into how a given receptor is converted to a fluorescent biosensor. Furthermore, we will demonstrate a significance of the modular strategy for the sensor design.
Collapse
|
50
|
Loving GS, Sainlos M, Imperiali B. Monitoring protein interactions and dynamics with solvatochromic fluorophores. Trends Biotechnol 2010; 28:73-83. [PMID: 19962774 PMCID: PMC2818466 DOI: 10.1016/j.tibtech.2009.11.002] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 11/03/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
Solvatochromic fluorophores possess emission properties that are sensitive to the nature of the local microenvironment. These dyes have been exploited in applications ranging from the study of protein structural dynamics to the detection of protein-binding interactions. Although the solvatochromic indole fluorophore of tryptophan has been utilized extensively for in vitro studies to advance our understanding of basic protein biochemistry, the emergence of new extrinsic synthetic dyes with improved properties, in conjunction with recent developments in site-selective methods to incorporate these chemical tools into proteins, now open the way for studies in more complex systems. Herein, we discuss recent technological advancements and their application in the design of powerful reporters, which serve critical roles in modern cell biology and assay development.
Collapse
Affiliation(s)
- Galen S Loving
- Department of Chemistry and Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
| | | | | |
Collapse
|