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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Recent advances in simultaneous thermostability-activity improvement of industrial enzymes through structure modification. Int J Biol Macromol 2023; 232:123440. [PMID: 36708895 DOI: 10.1016/j.ijbiomac.2023.123440] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Engineered thermostable microbial enzymes are widely employed to catalyze chemical reactions in numerous industrial sectors. Although high thermostability is a prerequisite of industrial applications, enzyme activity is usually sacrificed during thermostability improvement. Therefore, it is vital to select the common and compatible strategies between thermostability and activity improvement to reduce mutants̕ libraries and screening time. Three functional protein engineering approaches, including directed evolution, rational design, and semi-rational design, are employed to manipulate protein structure on a genetic basis. From a structural standpoint, integrative strategies such as increasing substrate affinity; introducing electrostatic interaction; removing steric hindrance; increasing flexibility of the active site; N- and C-terminal engineering; and increasing intramolecular and intermolecular hydrophobic interactions are well-known to improve simultaneous activity and thermostability. The current review aims to analyze relevant strategies to improve thermostability and activity simultaneously to circumvent the thermostability and activity trade-off of industrial enzymes.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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2
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Zhou X, Ma G, Wan Z, Wang S. Label-Free Multimetric Measurement of Molecular Binding Kinetics by Electrical Modulation of a Flexible Nanobiolayer. ACS Sens 2022; 7:3461-3469. [PMID: 36273329 PMCID: PMC10358282 DOI: 10.1021/acssensors.2c01804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Most label-free techniques rely on measuring refractive index or mass change on the sensor surface. Thus, it is challenging for them to measure small molecules or enzymatic processes that only induce a minor mass change on the analyte molecules. Here, we have developed a technique by combining Surface Plasmon Resonance sensing with an Oscillating Biomolecule Layer approach (SPR-OBL) to enhance the sensitivity of traditional SPR. In addition to the inherent mass sensitivity, SPR-OBL is also sensitive to the charge and conformational change of the analyte; hence it overcomes the mass limit and is able to detect small molecules. We show that the multimetric SPR-OBL measurement allows for sensing any changes regarding mass, charge, and conformation, which expands the detection capability of SPR.
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Affiliation(s)
- Xiaoyan Zhou
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, AZ 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Guangzhong Ma
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, AZ 85287, USA
| | - Zijian Wan
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, AZ 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Shaopeng Wang
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, AZ 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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Bajaj P, Manjunath K, Varadarajan R. Structural and functional determinants inferred from deep mutational scans. Protein Sci 2022; 31:e4357. [PMID: 35762712 DOI: 10.1002/pro.4357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/04/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022]
Abstract
Mutations that affect protein binding to a cognate partner primarily occur either at buried residues or at exposed residues directly involved in partner binding. Distinguishing between these two categories based solely on mutational phenotypes is challenging. The bacterial toxin CcdB kills cells by binding to DNA Gyrase. Cell death is prevented by binding to its cognate antitoxin CcdA, at an extended interface that partially overlaps with the GyrA binding site. Using the CcdAB toxin-antitoxin (TA) system as a model, a comprehensive site-saturation mutagenesis library of CcdB was generated in its native operonic context. The mutational sensitivity of each mutant was estimated by evaluating the relative abundance of each mutant in two strains, one resistant and the other sensitive to the toxic activity of the CcdB toxin, through deep sequencing. The ability to bind CcdA was inferred through a RelE reporter gene assay, since the CcdAB complex binds to its own promoter, repressing transcription. By analyzing mutant phenotypes in the CcdB-sensitive, CcdB-resistant, and RelE reporter strains, it was possible to assign residues to buried, CcdA interacting or GyrA interacting sites. A few mutants were individually constructed, expressed, and biophysically characterized to validate molecular mechanisms responsible for the observed phenotypes. Residues inferred to be important for antitoxin binding, are also likely to be important for rejuvenating CcdB from the CcdB-Gyrase complex. Therefore, even in the absence of structural information, when coupled to appropriate genetic screens, such high-throughput strategies can be deployed for predicting structural and functional determinants of proteins.
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Affiliation(s)
- Priyanka Bajaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology and Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
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4
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Preethi S, Arthiga K, Patil AB, Spandana A, Jain V. Review on NAD(P)H dehydrogenase quinone 1 (NQO1) pathway. Mol Biol Rep 2022; 49:8907-8924. [PMID: 35347544 DOI: 10.1007/s11033-022-07369-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/11/2022] [Indexed: 12/14/2022]
Abstract
NQO1 is an enzyme present in humans which is encoded by NQO1 gene. It is a protective antioxidant agent, versatile cytoprotective agent and regulates the oxidative stresses of chromatin binding proteins for DNA damage in cancer cells. The oxidization of cellular pyridine nucleotides causes structural alterations to NQO1 and changes in its capacity to binding of proteins. A strategy based on NQO1 to have protective effect against cancer was developed by organic components to enhance NQO1 expression. The quinone derivative compounds like mitomycin C, RH1, E09 (Apaziquone) and β-lapachone causes cell death by NQO1 reduction of two electrons. It was also known to be overexpressed in various tumor cells of breast, lung, cervix, pancreas and colon when it was compared with normal cells in humans. The mechanism of NQO1 by the reduction of FAD by NADPH to form FADH2 is by two ways to inhibit cancer cell development such as suppression of carcinogenic metabolic activation and prevention of carcinogen formation. The NQO1 exhibit suppression of chemical-mediated carcinogenesis by various properties of NQO1 which includes, detoxification of quinone scavenger of superoxide anion radical, antioxidant enzyme, protein stabilizer. This review outlines the NQO1 structure, mechanism of action to inhibit the cancer cell, functions of NQO1 against oxidative stress, drugs acting on NQO1 pathways, clinical significance.
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Affiliation(s)
- S Preethi
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysuru, Karnataka, 570015, India
| | - K Arthiga
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysuru, Karnataka, 570015, India
| | - Amit B Patil
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysuru, Karnataka, 570015, India
| | - Asha Spandana
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysuru, Karnataka, 570015, India
| | - Vikas Jain
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysuru, Karnataka, 570015, India.
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5
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Hao M, Cui R, Zhu X, Han L, Zhou Z, Liu Z. Improving the activity and synergistic catalysis of l-aspartate β-decarboxylase by arginine introduction on the surface. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00700b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction of arginine on the surface relieved the pH-dependent inactivation of l-aspartate-β-decarboxylase, which promoted its application in synthetic biology and biocatalysis.
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Affiliation(s)
- Mingzhu Hao
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
| | - Ruizhi Cui
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
| | - Xiaoqing Zhu
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
| | - Laichuang Han
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, China
| | - Zhongmei Liu
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, China
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6
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Carvalho HF, Ferrario V, Pleiss J. Molecular Mechanism of Methanol Inhibition in CALB-Catalyzed Alcoholysis: Analyzing Molecular Dynamics Simulations by a Markov State Model. J Chem Theory Comput 2021; 17:6570-6582. [PMID: 34494846 DOI: 10.1021/acs.jctc.1c00559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipases are widely used enzymes that catalyze hydrolysis and alcoholysis of fatty acid esters. At high concentrations of small alcohols such as methanol or ethanol, many lipases are inhibited by the substrate. The molecular basis of the inhibition of Candida antarctica lipase B (CALB) by methanol was investigated by unbiased molecular dynamics (MD) simulations, and the substrate binding kinetics was analyzed by Markov state models (MSMs). The modeled fluxes of productive methanol binding at concentrations between 50 mM and 5.5 M were in good agreement with the experimental activity profile of CALB, with a peak at 300 mM. The kinetic and structural analysis uncovered the molecular basis of CALB inhibition. Beyond 300 mM, the kinetic bottleneck results from crowding of methanol in the substrate access channel, which is caused by the gradual formation of methanol patches close to Leu140 (helix α5), Leu278, and Ile285 (helix α10) at a distance of 4-5 Å from the active site. Our findings demonstrate the usefulness of unbiased MD simulations to study enzyme-substrate interactions at realistic substrate concentrations and the feasibility of scale-bridging by an MSM analysis to derive kinetic information.
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Affiliation(s)
- Henrique F Carvalho
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Lisitsa AE, Sukovatyi LA, Bartsev SI, Deeva AA, Kratasyuk VA, Nemtseva EV. Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction. Int J Mol Sci 2021; 22:8827. [PMID: 34445534 PMCID: PMC8396235 DOI: 10.3390/ijms22168827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial bioluminescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. Moreover, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important αGlu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis.
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Affiliation(s)
- Albert E Lisitsa
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Lev A Sukovatyi
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Sergey I Bartsev
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Anna A Deeva
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Valentina A Kratasyuk
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Elena V Nemtseva
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
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8
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Odenkirk MT, Reif DM, Baker ES. Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. Anal Chem 2021; 93:7763-7773. [PMID: 34029068 PMCID: PMC8465926 DOI: 10.1021/acs.analchem.0c04850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The need for holistic molecular measurements to better understand disease initiation, development, diagnosis, and therapy has led to an increasing number of multiomic analyses. The wealth of information available from multiomic assessments, however, requires both the evaluation and interpretation of extremely large data sets, limiting analysis throughput and ease of adoption. Computational methods utilizing artificial intelligence (AI) provide the most promising way to address these challenges, yet despite the conceptual benefits of AI and its successful application in singular omic studies, the widespread use of AI in multiomic studies remains limited. Here, we discuss present and future capabilities of AI techniques in multiomic studies while introducing analytical checks and balances to validate the computational conclusions.
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Affiliation(s)
- Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - David M Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27606, United States
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, United States
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Verma R, Ellis JM, Mitchell-Koch KR. Dynamic Preference for NADP/H Cofactor Binding/Release in E. coli YqhD Oxidoreductase. Molecules 2021; 26:E270. [PMID: 33430436 PMCID: PMC7826944 DOI: 10.3390/molecules26020270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/16/2022] Open
Abstract
YqhD, an E. coli alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release. The ensemble of NADPH-bound monomers has a narrower average interdomain space resulting in more hydrogen bonds and rigid cofactor binding. NADP-bound YqhD fluctuates between open and closed conformations, while it was observed that NADPH-bound YqhD had slower opening/closing dynamics of the cofactor-binding cleft. In the light of enzyme kinetics and structural data, simulation findings have led us to postulate that the frequently sampled open conformation of the cofactor binding cleft with NADP leads to the more facile release of NADP while increased closed conformation sampling during NADPH binding enhances cofactor binding affinity and the aldehyde reductase activity of the enzyme.
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Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260, USA
| | - Jonathan M. Ellis
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA;
| | - Katie R. Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260, USA
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10
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Seyedhosseini Ghaheh H, Ganjalikhany MR, Yaghmaei P, Pourfarzam M, Mir Mohammad Sadeghi H. Investigation of Supercharging as A Strategy to Enhance the Solubility and Plasminogen Cleavage Activity of Reteplase. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2556. [PMID: 34056023 PMCID: PMC8148640 DOI: 10.30498/ijb.2020.2556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Reteplase, the recombinant form of tissue plasminogen activator, is a thrombolytic drug with outstanding characteristics, while demonstrating limited solubility and reduced plasminogen activation. Previously, we in silico designed a variant of Reteplase with positively supercharged surface, which showed promising stability, solubility and activity. This study was devoted to evaluation of the utility of supercharging technique for enhancing these characteristics in Reteplase. Objective To test the hypothesis that reinforced surface charge of a rationally-designed Reteplase variant will not compromise its stability, will increase its solubility, and will enhance its plasminogen cleavage activity. Materials and Methods Supercharged Reteplase coding sequence was cloned in pDest527 vector and expressed in E. coli BL21 (DE3). The expressed protein was extracted by cell disruption. Inclusion bodies were solubilized using guanidine hydrochloride, followed by dialysis for protein refolding. After confirmation with SDS-PAGE and western blotting, extracted proteins were assayed for solubility and tested for bioactivity. Results SDS-PAGE and western blot analysis confirmed the successful expression of Reteplase. Western blot experiments showed most of Reteplase expressed in the insoluble form. Plasminogen cleavage assay showed significantly higher activity of the supercharged variant than the wild type protein (P < 0.001). The stability of the supercharged variant was also comparable to the wild type. Conclusion Our findings, i.e. the contribution of the surface supercharging technique to retained stability, enhanced plasminogen cleavage activity, while inefficiently changed solubility of Reteplase, contain implications for future designs of soluble variants of this fibrinolytic protein drug.
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Affiliation(s)
| | | | - Parichehreh Yaghmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Morteza Pourfarzam
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Mir Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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Smith NL, Coukouma AE, Wilson DC, Ho B, Gray V, Asher SA. Stimuli-Responsive Pure Protein Organogel Sensors and Biocatalytic Materials. ACS APPLIED MATERIALS & INTERFACES 2020; 12:238-249. [PMID: 31820639 DOI: 10.1021/acsami.9b18191] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Utilizing protein chemistry in organic solvents has important biotechnology applications. Typically, organic solvents negatively impact protein structure and function. Immobilizing proteins via cross-links to a support matrix or to other proteins is a common strategy to preserve the native protein function. Recently, we developed methods to fabricate macroscopic responsive pure protein hydrogels by lightly cross-linking the proteins with glutaraldehyde for chemical sensing and enzymatic catalysis applications. The water in the resulting protein hydrogel can be exchanged for organic solvents. The resulting organogel contains pure organic solvents as their mobile phases. The organogel proteins retain much of their native protein function, i.e., protein-ligand binding and enzymatic activity. A stepwise ethylene glycol (EG) solvent exchange was performed to transform these hydrogels into organogels with a very low vapor pressure mobile phase. These responsive organogels are not limited by solvent/mobile phase evaporation. The solvent exchange to pure EG is accompanied by a volume phase transition (VPT) that decreases the organogel volume compared to that of the hydrogel. Our organogel sensor systems utilize shifts in the particle spacing of an attached two-dimensional photonic crystal (2DPC) to report on the volume changes induced by protein-ligand binding. Our 2DPC bovine serum albumin (BSA) organogels exhibit VPT that swell the organogels in response to the BSA binding of charged ligands like ibuprofen and fatty acids. To our knowledge, this is the first report of a pure protein organogel VPT induced by protein-ligand binding. Catalytic protein organogels were also fabricated that utilize the enzyme organophosphorus hydrolase (OPH) to hydrolyze toxic organophosphate (OP) nerve agents. Our OPH organogels retain significant enzymatic activity. The OPH organogel rate of OP hydrolysis is ∼160 times higher than that of un-cross-linked OPH monomers in a 1:1 ethylene glycol/water mixture.
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Affiliation(s)
- Natasha L Smith
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Andrew E Coukouma
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - David C Wilson
- FLIR Systems Inc. , Pittsburgh , Pennsylvania 15238 , United States
| | - Brenda Ho
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Vincent Gray
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Sanford A Asher
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
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Dahanayake JN, Mitchell-Koch KR. How Does Solvation Layer Mobility Affect Protein Structural Dynamics? Front Mol Biosci 2018; 5:65. [PMID: 30057902 PMCID: PMC6053501 DOI: 10.3389/fmolb.2018.00065] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.
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Chegkazi MS, Mamais M, Sotiropoulou AI, Chrysina ED. Rational Drug Design Using Integrative Structural Biology. Methods Mol Biol 2018; 1824:89-111. [PMID: 30039403 DOI: 10.1007/978-1-4939-8630-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Modern drug discovery and design approaches rely heavily on high-throughput methods and state-of-the-art infrastructures with robotic facilities and sophisticated platforms. However, the anticipated research output that would eventually lead to new drugs with minimal or no side effects to the market has not been achieved. Despite the vast amount of information generated, very little is converted to knowledge and even less is capitalized for cross-discipline research actions. Therefore, the need for re-launching rational approaches has become apparent. Here we present an overview of the new trends in rational drug design using integrative structural biology with emphasis on X-ray protein crystallography and small molecules as ligands. With the aim to increase researchers' awareness on the available possibilities to perform front line research, we also underline the benefits and enhanced prospects offered to the scientific community, through access to research infrastructures.
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Affiliation(s)
- Magda S Chegkazi
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Faculty of Life Sciences and Medicine, Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Michael Mamais
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia I Sotiropoulou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
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