1
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Herman RA, Ayepa E, Zhang WX, Li ZN, Zhu X, Ackah M, Yuan SS, You S, Wang J. Molecular modification and biotechnological applications of microbial aspartic proteases. Crit Rev Biotechnol 2024; 44:388-413. [PMID: 36842994 DOI: 10.1080/07388551.2023.2171850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 12/13/2022] [Accepted: 01/07/2023] [Indexed: 02/28/2023]
Abstract
The growing preference for incorporating microbial aspartic proteases in industries is due to their high catalytic function and high degree of substrate selectivity. These properties, however, are attributable to molecular alterations in their structure and a variety of other characteristics. Molecular tools, functional genomics, and genome editing technologies coupled with other biotechnological approaches have aided in improving the potential of industrially important microbial proteases by addressing some of their major limitations, such as: low catalytic efficiency, low conversion rates, low thermostability, and less enzyme yield. However, the native folding within their full domain is dependent on a surrounding structure which challenges their functionality in substrate conversion, mainly due to their mutual interactions in the context of complex systems. Hence, manipulating their structure and controlling their expression systems could potentially produce enzymes with high selectivity and catalytic functions. The proteins produced by microbial aspartic proteases are industrially capable and far-reaching in regulating certain harmful distinctive industrial processes and the benefits of being eco-friendly. This review provides: an update on current trends and gaps in microbial protease biotechnology, exploring the relevant recombinant strategies and molecular technologies widely used in expression platforms for engineering microbial aspartic proteases, as well as their potential industrial and biotechnological applications.
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Affiliation(s)
- Richard Ansah Herman
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- School of Materials Science and Engineering, Jiangsu University of Science and Technology, Zhenjiang, P. R. China
| | - Ellen Ayepa
- Oil Palm Research Institute, Council for Scientific and Industrial Research, Kusi, Ghana
| | - Wen-Xin Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Zong-Nan Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Xuan Zhu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Michael Ackah
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Shuang-Shuang Yuan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Shuai You
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, P.R. China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, P.R. China
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2
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Ó'Fágáin C. Protein Stability: Enhancement and Measurement. Methods Mol Biol 2023; 2699:369-419. [PMID: 37647007 DOI: 10.1007/978-1-0716-3362-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin, Ireland.
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3
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Atsavapranee B, Stark CD, Sunden F, Thompson S, Fordyce PM. Fundamentals to function: Quantitative and scalable approaches for measuring protein stability. Cell Syst 2021; 12:547-560. [PMID: 34139165 DOI: 10.1016/j.cels.2021.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/16/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Folding a linear chain of amino acids into a three-dimensional protein is a complex physical process that ultimately confers an impressive range of diverse functions. Although recent advances have driven significant progress in predicting three-dimensional protein structures from sequence, proteins are not static molecules. Rather, they exist as complex conformational ensembles defined by energy landscapes spanning the space of sequence and conditions. Quantitatively mapping the physical parameters that dictate these landscapes and protein stability is therefore critical to develop models that are capable of predicting how mutations alter function of proteins in disease and informing the design of proteins with desired functions. Here, we review the approaches that are used to quantify protein stability at a variety of scales, from returning multiple thermodynamic and kinetic measurements for a single protein sequence to yielding indirect insights into folding across a vast sequence space. The physical parameters derived from these approaches will provide a foundation for models that extend beyond the structural prediction to capture the complexity of conformational ensembles and, ultimately, their function.
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Affiliation(s)
| | - Catherine D Stark
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Samuel Thompson
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
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4
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Moore-Kelly C, Welsh J, Rodger A, Dafforn TR, Thomas ORT. Automated High-Throughput Capillary Circular Dichroism and Intrinsic Fluorescence Spectroscopy for Rapid Determination of Protein Structure. Anal Chem 2019; 91:13794-13802. [PMID: 31584804 PMCID: PMC7006967 DOI: 10.1021/acs.analchem.9b03259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
Assessing
the physical stability of proteins is one of the most
important challenges in the development, manufacture, and formulation
of biotherapeutics. Here, we describe a method for combining and automating
circular dichroism and intrinsic protein fluorescence spectroscopy.
By robotically injecting samples from a 96-well plate into an optically
compliant capillary flow cell, complementary information about the
secondary and tertiary structural state of a protein can be collected
in an unattended manner from considerably reduced volumes of sample
compared to conventional techniques. We demonstrate the accuracy and
reproducibility of this method. Furthermore, we show how structural
screening can be used to monitor unfolding of proteins in two case
studies using (i) a chaotropic denaturant (urea) and (ii) low-pH buffers
used for monoclonal antibody (mAb) purification during Protein A chromatography.
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Affiliation(s)
| | - John Welsh
- Pall Biotech , Southampton Road , Portsmouth , PO6 4BQ , U.K
| | - Alison Rodger
- Department of Molecular Sciences , Macquarie University , Macquarie Park , Sydney , New South Wales 2109 , Australia
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5
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Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis. Proc Natl Acad Sci U S A 2019; 116:16367-16377. [PMID: 31371509 DOI: 10.1073/pnas.1903888116] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The accurate prediction of protein stability upon sequence mutation is an important but unsolved challenge in protein engineering. Large mutational datasets are required to train computational predictors, but traditional methods for collecting stability data are either low-throughput or measure protein stability indirectly. Here, we develop an automated method to generate thermodynamic stability data for nearly every single mutant in a small 56-residue protein. Analysis reveals that most single mutants have a neutral effect on stability, mutational sensitivity is largely governed by residue burial, and unexpectedly, hydrophobics are the best tolerated amino acid type. Correlating the output of various stability-prediction algorithms against our data shows that nearly all perform better on boundary and surface positions than for those in the core and are better at predicting large-to-small mutations than small-to-large ones. We show that the most stable variants in the single-mutant landscape are better identified using combinations of 2 prediction algorithms and including more algorithms can provide diminishing returns. In most cases, poor in silico predictions were tied to compositional differences between the data being analyzed and the datasets used to train the algorithm. Finally, we find that strategies to extract stabilities from high-throughput fitness data such as deep mutational scanning are promising and that data produced by these methods may be applicable toward training future stability-prediction tools.
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6
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Seal S, Polley S, Sau S. A staphylococcal cyclophilin carries a single domain and unfolds via the formation of an intermediate that preserves cyclosporin A binding activity. PLoS One 2019; 14:e0210771. [PMID: 30925148 PMCID: PMC6440624 DOI: 10.1371/journal.pone.0210771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/18/2019] [Indexed: 12/22/2022] Open
Abstract
Cyclophilin (Cyp), a peptidyl-prolyl cis-trans isomerase (PPIase), acts as a virulence factor in many bacteria including Staphylococcus aureus. The enzymatic activity of Cyp is inhibited by cyclosporin A (CsA), an immunosuppressive drug. To precisely determine the unfolding mechanism and the domain structure of Cyp, we have investigated a chimeric S. aureus Cyp (rCyp) using various probes. Our limited proteolysis and the consequent analysis of the proteolytic fragments indicate that rCyp is composed of one domain with a short flexible tail at the C-terminal end. We also show that the urea-induced unfolding of both rCyp and rCyp-CsA is completely reversible and proceeds via the synthesis of at least one stable intermediate. Both the secondary structure and the tertiary structure of each intermediate appears very similar to those of the corresponding native protein. Conversely, the hydrophobic surface areas of the intermediates are comparatively less. Further analyses reveal no loss of CsA binding activity in rCyp intermediate. The thermodynamic stability of rCyp was also significantly increased in the presence of CsA, recommending that this protein could be employed to screen new CsA derivatives in the future.
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Affiliation(s)
- Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail:
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7
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A method for rapid high-throughput biophysical analysis of proteins. Sci Rep 2017; 7:9071. [PMID: 28831058 PMCID: PMC5567296 DOI: 10.1038/s41598-017-08664-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/14/2017] [Indexed: 11/09/2022] Open
Abstract
Quantitative determination of protein thermodynamic stability is fundamental to many research areas, both basic and applied. Although chemical-induced denaturation is the gold-standard method, it has been replaced in many settings by semi-quantitative approaches such as thermal stability measurements. The reason for this shift is that chemical denaturation experiments are labour-intensive, sample-costly and time-consuming, and it has been assumed that miniaturisation to a high-throughput format would not be possible without concomitantly comprising data quality. Here we exploit current technologies to create a high-throughput label-free chemical denaturation method that is capable of generating replicate datasets on multiple proteins in parallel on a timescale that is at least ten times faster, much more economical on sample, and with the potential for superior data quality, than the conventional methods used in most research labs currently.
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8
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Abstract
This article defines protein stability, emphasizes its importance and surveys the field of protein stabilization, with summary reference to a selection of 2009-2015 publications. One can enhance stability by, in particular, protein engineering strategies and by chemical modification (including conjugation) in solution. General protocols are set out on how to measure a given protein's (1) kinetic thermal stability, and (2) oxidative stability, and (3) how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland.
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9
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Wang Q, Waterhouse N, Feyijinmi O, Dominguez MJ, Martinez LM, Sharp Z, Service R, Bothe JR, Stollar EJ. Development and Application of a High Throughput Protein Unfolding Kinetic Assay. PLoS One 2016; 11:e0146232. [PMID: 26745729 PMCID: PMC4706425 DOI: 10.1371/journal.pone.0146232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 12/15/2015] [Indexed: 11/18/2022] Open
Abstract
The kinetics of folding and unfolding underlie protein stability and quantification of these rates provides important insights into the folding process. Here, we present a simple high throughput protein unfolding kinetic assay using a plate reader that is applicable to the studies of the majority of 2-state folding proteins. We validate the assay by measuring kinetic unfolding data for the SH3 (Src Homology 3) domain from Actin Binding Protein 1 (AbpSH3) and its stabilized mutants. The results of our approach are in excellent agreement with published values. We further combine our kinetic assay with a plate reader equilibrium assay, to obtain indirect estimates of folding rates and use these approaches to characterize an AbpSH3-peptide hybrid. Our high throughput protein unfolding kinetic assays allow accurate screening of libraries of mutants by providing both kinetic and equilibrium measurements and provide a means for in-depth ϕ-value analyses.
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Affiliation(s)
- Qiang Wang
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Nicklas Waterhouse
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Olusegun Feyijinmi
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Matthew J. Dominguez
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Lisa M. Martinez
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Zoey Sharp
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Rachel Service
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
| | - Jameson R. Bothe
- NMRFAM, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elliott J. Stollar
- Department of Physical Sciences, Eastern New Mexico University, Portales, New Mexico, United States of America
- * E-mail:
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10
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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11
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Noyes A, Huffman B, Berrill A, Merchant N, Godavarti R, Titchener-Hooker N, Coffman J, Sunasara K, Mukhopadhyay T. High throughput screening of particle conditioning operations: II. Evaluation of scale-up heuristics with prokaryotically expressed polysaccharide vaccines. Biotechnol Bioeng 2015; 112:1568-82. [PMID: 25727194 DOI: 10.1002/bit.25580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 02/15/2015] [Accepted: 02/17/2015] [Indexed: 11/08/2022]
Abstract
Multivalent polysaccharide conjugate vaccines are typically comprised of several different polysaccharides produced with distinct and complex production processes. Particle conditioning steps, such as precipitation and flocculation, may be used to aid the recovery and purification of such microbial vaccine products. An ultra scale-down approach to purify vaccine polysaccharides at the micro-scale would greatly enhance productivity, robustness, and speed the development of novel conjugate vaccines. In part one of this series, we described a modular and high throughput approach to develop particle conditioning processes (HTPC) for biologicals that combines flocculation, solids removal, and streamlined analytics. In this second part of the series, we applied HTPC to industrially relevant feedstreams comprised of capsular polysaccharides (CPS) from several bacterial species. The scalability of HTPC was evaluated between 0.8 mL and 13 L scales, with several different scaling methodologies examined. Clarification, polysaccharide yield, impurity clearance, and product quality achieved with HTPC were reproducible and comparable with larger scales. Particle sizing was the response with greatest sensitivity to differences in processing scale and enabled the identification of useful scaling rules. Scaling with constant impeller tip speed or power per volume in the impeller swept zone offered the most accurate scale up, with evidence that time integration of these values provided the optimal basis for scaling. The capability to develop a process at the micro-scale combined with evidence-based scaling metrics provide a significant advance for purification process development of vaccine processes. The USD system offers similar opportunities for HTPC of proteins and other complex biological molecules.
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Affiliation(s)
- Aaron Noyes
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London, WC1E 7JE, UK.,Pfizer Bioprocess R&D, Andover, Massachusetts
| | - Ben Huffman
- Pfizer Bioprocess R&D, Chesterfield, Missouri
| | | | | | | | - Nigel Titchener-Hooker
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London, WC1E 7JE, UK
| | | | | | - Tarit Mukhopadhyay
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London, WC1E 7JE, UK.
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12
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Larsen HML, Trnka H, Grohganz H. Formation of mannitol hemihydrate in freeze-dried protein formulations—A design of experiment approach. Int J Pharm 2014; 460:45-52. [DOI: 10.1016/j.ijpharm.2013.11.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/31/2013] [Accepted: 11/05/2013] [Indexed: 11/15/2022]
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13
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Guca E, Roumestand C, Vallone B, Royer CA, Dellarole M. Low-cost equilibrium unfolding of heme proteins using 2 μl samples. Anal Biochem 2013; 443:13-5. [DOI: 10.1016/j.ab.2013.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/06/2013] [Accepted: 08/08/2013] [Indexed: 11/16/2022]
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14
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Nashine VC, Kroetsch AM, Sahin E, Zhou R, Adams ML. Orthogonal high-throughput thermal scanning method for rank ordering protein formulations. AAPS PharmSciTech 2013; 14:1360-6. [PMID: 24002823 DOI: 10.1208/s12249-013-0026-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/20/2013] [Indexed: 11/30/2022] Open
Abstract
A high-throughput thermal-scanning method to rank-order formulation conditions for therapeutic proteins is described. Apparent transition temperatures for unfolding and aggregation of four different proteins are determined using the dyes SYPRO Orange and thioflavin T (ThT) under a variety of buffer conditions. The results indicate that the ThT-based thermal scanning method offers several advantages over the previously described SYPRO Orange-based thermal scanning and allows rapid rank ordering of solution conditions relevant toward long-term storage of therapeutic molecules. The method is also amenable to high protein concentration and does not require sample dilution or extensive preparation. Additionally, this parallel use of SYPRO Orange and ThT can be readily applied to the screening of mutants for their unfolding and aggregation propensities.
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15
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Sagar DM, Aoudjane S, Gaudet M, Aeppli G, Dalby PA. Optically induced thermal gradients for protein characterization in nanolitre-scale samples in microfluidic devices. Sci Rep 2013; 3:2130. [PMID: 23823279 PMCID: PMC3703920 DOI: 10.1038/srep02130] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/30/2013] [Indexed: 11/16/2022] Open
Abstract
Proteins are the most vital biological functional units in every living cell. Measurement
of protein stability is central to understanding their structure, function and role in
diseases. While proteins are also sought as therapeutic agents, they can cause diseases by
misfolding and aggregation in vivo. Here we demonstrate a novel method to measure protein
stability and denaturation kinetics, on unprecedented timescales, through optically-induced
heating of nanolitre samples in microfluidic capillaries. We obtain protein denaturation
kinetics as a function of temperature, and accurate thermodynamic stability data, from a
snapshot experiment on a single sample. We also report the first experimental
characterization of optical heating in controlled microcapillary flow, verified by
computational fluid dynamics modelling. Our results demonstrate that we now have the
engineering science in hand to design integrated all-optical microfluidic chips for a
diverse range of applications including in-vitro DNA amplification, healthcare diagnostics,
and flow chemistry.
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Affiliation(s)
- D M Sagar
- Department of Biochemical Engineering, Torrington Place, University College London, London, WC1E 7JE, UK
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16
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Freire E, Schön A, Hutchins BM, Brown RK. Chemical denaturation as a tool in the formulation optimization of biologics. Drug Discov Today 2013; 18:1007-13. [PMID: 23796912 DOI: 10.1016/j.drudis.2013.06.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 05/24/2013] [Accepted: 06/14/2013] [Indexed: 10/26/2022]
Abstract
Biologics have become the fastest growing segment in the pharmaceutical industry. As is the case with all proteins, biologics are susceptible to denature or to aggregate; conditions that, if present, preclude their use as pharmaceuticals. Identifying the solvent conditions that maximize their structural stability is crucial during development. Since the structural stability of a protein is susceptible to different chemical and physical conditions, the use of several complementary techniques can be expected to provide the best answers. Stability measurements that rely on temperature or chemical [urea or guanidine hydrochloride (GuHCl)] denaturation have been the preferred ones in research laboratories and together provide a thorough evaluation of protein stability. In this review, we will discuss chemical denaturation as a tool in the optimization of formulation conditions for biologics, and how chemical denaturation complements the role of thermal denaturation for this purpose.
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Affiliation(s)
- Ernesto Freire
- AVIA Biosystems, 775 East Falmouth Highway, Suite 193, East Falmouth, MA 02536, USA
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17
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Buchanan A, Clementel V, Woods R, Harn N, Bowen MA, Mo W, Popovic B, Bishop SM, Dall'Acqua W, Minter R, Jermutus L, Bedian V. Engineering a therapeutic IgG molecule to address cysteinylation, aggregation and enhance thermal stability and expression. MAbs 2013; 5:255-62. [PMID: 23412563 PMCID: PMC3893235 DOI: 10.4161/mabs.23392] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Antibodies can undergo a variety of covalent and non-covalent degradation reactions that have adverse effects on efficacy, safety, manufacture and storage. We had identified an antibody to Angiopoietin 2 (Ang2 mAb) that neutralizes Ang2 binding to its receptor in vitro and inhibits tumor growth in vivo. Despite favorable pharmacological activity, the Ang2 mAb preparations were heterogeneous, aggregated rapidly and were poorly expressed. Here, we report the engineering of the antibody variable and constant domains to generate an antibody with reduced propensity to aggregate, enhanced homogeneity, 11°C elevated T(m), 26-fold improved level of expression and retained activity. The engineered molecule, MEDI-3617, is now compatible with the large scale material supply required for clinical trials and is currently being evaluated in Phase 1 in cancer patients. This is the first report to describe the stability engineering of a therapeutic antibody addressing non canonical cysteine residues and the design strategy reported here is generally applicable to other therapeutic antibodies and proteins.
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18
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Sullivan BJ, Nguyen T, Durani V, Mathur D, Rojas S, Thomas M, Syu T, Magliery TJ. Stabilizing proteins from sequence statistics: the interplay of conservation and correlation in triosephosphate isomerase stability. J Mol Biol 2012; 420:384-99. [PMID: 22555051 DOI: 10.1016/j.jmb.2012.04.025] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/16/2012] [Accepted: 04/21/2012] [Indexed: 10/28/2022]
Abstract
Understanding the determinants of protein stability remains one of protein science's greatest challenges. There are still no computational solutions that calculate the stability effects of even point mutations with sufficient reliability for practical use. Amino acid substitutions rarely increase the stability of native proteins; hence, large libraries and high-throughput screens or selections are needed to stabilize proteins using directed evolution. Consensus mutations have proven effective for increasing stability, but these mutations are successful only about half the time. We set out to understand why some consensus mutations fail to stabilize, and what criteria might be useful to predict stabilization more accurately. Overall, consensus mutations at more conserved positions were more likely to be stabilizing in our model, triosephosphate isomerase (TIM) from Saccharomyces cerevisiae. However, positions coupled to other sites were more likely not to stabilize upon mutation. Destabilizing mutations could be removed both by removing sites with high statistical correlations to other positions and by removing nearly invariant positions at which "hidden correlations" can occur. Application of these rules resulted in identification of stabilizing mutations in 9 out of 10 positions, and amalgamation of all predicted stabilizing positions resulted in the most stable yeast TIM variant we produced (+8 °C). In contrast, a multimutant with 14 mutations each found to stabilize TIM independently was destabilized by 2 °C. Our results are a practical extension to the consensus concept of protein stabilization, and they further suggest the importance of positional independence in the mechanism of consensus stabilization.
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Affiliation(s)
- Brandon J Sullivan
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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19
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Ordidge GC, Mannall G, Liddell J, Dalby PA, Micheletti M. A generic hierarchical screening method for the analysis of microscale refolds using an automated robotic platform. Biotechnol Prog 2012; 28:435-44. [DOI: 10.1002/btpr.1502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 11/21/2011] [Indexed: 11/07/2022]
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20
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Grant Y, Matejtschuk P, Bird C, Wadhwa M, Dalby PA. Freeze drying formulation using microscale and design of experiment approaches: a case study using granulocyte colony-stimulating factor. Biotechnol Lett 2011; 34:641-8. [DOI: 10.1007/s10529-011-0822-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 11/29/2011] [Indexed: 10/14/2022]
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21
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Dasnoy S, Le Bras V, Préat V, Lemoine D. High-throughput assessment of antigen conformational stability by ultraviolet absorption spectroscopy and its application to excipient screening. Biotechnol Bioeng 2011; 109:502-16. [DOI: 10.1002/bit.23336] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/31/2011] [Accepted: 09/06/2011] [Indexed: 11/11/2022]
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22
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Ahmad I, Sheraz MA, Ahmed S, Shaikh RH, Vaid FHM, ur Rehman Khattak S, Ansari SA. Photostability and interaction of ascorbic acid in cream formulations. AAPS PharmSciTech 2011; 12:917-23. [PMID: 21735345 DOI: 10.1208/s12249-011-9659-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 06/28/2011] [Indexed: 11/30/2022] Open
Abstract
The kinetics of photolysis of ascorbic acid in cream formulations on UV irradiation has been studied using a specific spectrophotometric method with a reproducibility of ± 5%. The apparent first-order rate constants (k(obs)) for the photolysis of ascorbic acid in creams have been determined. The photoproducts formed in the cream formulations include dehydroascorbic acid and 2,3-diketogulonic acid. The photolysis of ascorbic acid appears to be affected by the concentration of active ingredient, pH, and viscosity of the medium and formulation characteristics. The study indicates that the ionized state and redox potentials of ascorbic acid are important factors in the photostability of the vitamin in cream formulations. The viscosity of the humectant present in the creams appears to influence the photostability of ascorbic acid. The results show that the physical stability of the creams is an important factor in the stabilization of the vitamin. In the cream formulations stored in the dark, ascorbic acid undergoes aerobic oxidation and the degradation is affected by similar factors as indicated in the photolysis reactions. The rate of oxidative degradation in the dark is about seventy times slower than that observed in the presence of light.
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23
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Magliery TJ, Lavinder JJ, Sullivan BJ. Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems. Curr Opin Chem Biol 2011; 15:443-51. [PMID: 21498105 DOI: 10.1016/j.cbpa.2011.03.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/18/2011] [Accepted: 03/18/2011] [Indexed: 01/24/2023]
Abstract
Most proteins are only barely stable, which impedes research, complicates therapeutic applications, and makes proteins susceptible to pathologically destabilizing mutations. Our ability to predict the thermodynamic consequences of even single point mutations is still surprisingly limited, and established methods of measuring stability are slow. Recent advances are bringing protein stability studies into the high-throughput realm. Some methods are based on inferential read-outs such as activity, proteolytic resistance or split-protein fragment reassembly. Other methods use miniaturization of direct measurements, such as intrinsic fluorescence, H/D exchange, cysteine reactivity, aggregation and hydrophobic dye binding (DSF). Protein engineering based on statistical analysis (consensus and correlated occurrences of amino acids) is promising, but much work remains to understand and implement these methods.
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Affiliation(s)
- Thomas J Magliery
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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24
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Mahendrarajah K, Dalby PA, Wilkinson B, Jackson SE, Main ER. A high-throughput fluorescence chemical denaturation assay as a general screen for protein–ligand binding. Anal Biochem 2011; 411:155-7. [DOI: 10.1016/j.ab.2010.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 11/26/2022]
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25
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Abstract
This article defines protein stability, emphasizes its importance and surveys some notable recent publications (2004-2008) in the field of protein stability/stabilization. Knowledge of the factors stabilizing proteins has emerged from denaturation studies and from study of thermophilic (and other extremophilic) proteins. One can enhance stability by protein engineering strategies, the judicious use of solutes and additives, immobilization, and chemical modification in solution. General protocols are set out on how to measure the kinetic thermal stability of a given protein and how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán O'Fágáin
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
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26
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Gaudet M, Remtulla N, Jackson SE, Main ERG, Bracewell DG, Aeppli G, Dalby PA. Protein denaturation and protein:drugs interactions from intrinsic protein fluorescence measurements at the nanolitre scale. Protein Sci 2010; 19:1544-54. [PMID: 20552687 DOI: 10.1002/pro.433] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein stability and ligand-binding affinity measurements are widely required for the formulation of biopharmaceutical proteins, protein engineering and drug screening within life science research. Current techniques either consume too much of often precious biological or compound materials, in large sample volumes, or alternatively require chemical labeling with fluorescent tags to achieve measurements at submicrolitre volumes with less sample. Here we present a quantitative and accurate method for the determination of protein stability and the affinity for small molecules, at only 1.5-20 nL optical sample volumes without the need for fluorescent labeling, and that takes advantage of the intrinsic tryptophan fluorescence of most proteins. Coupled to appropriate microfluidic sample preparation methods, the sample requirements could thus be reduced 85,000-fold to just 10(8) molecules. The stability of wild-type FKBP-12 and a destabilizing binding-pocket mutant are studied in the presence and absence of rapamycin, to demonstrate the potential of the technique to both drug screening and protein engineering. The results show that 75% of the interaction energy between FKBP-12 and rapamycin originates from residue Phe99 in the binding site.
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Affiliation(s)
- Matthieu Gaudet
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
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Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles. Proc Natl Acad Sci U S A 2010; 107:19838-43. [PMID: 21045132 DOI: 10.1073/pnas.1012985107] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The stability, activity, and solubility of a protein sequence are determined by a delicate balance of molecular interactions in a variety of conformational states. Even so, most computational protein design methods model sequences in the context of a single native conformation. Simulations that model the native state as an ensemble have been mostly neglected due to the lack of sufficiently powerful optimization algorithms for multistate design. Here, we have applied our multistate design algorithm to study the potential utility of various forms of input structural data for design. To facilitate a more thorough analysis, we developed new methods for the design and high-throughput stability determination of combinatorial mutation libraries based on protein design calculations. The application of these methods to the core design of a small model system produced many variants with improved thermodynamic stability and showed that multistate design methods can be readily applied to large structural ensembles. We found that exhaustive screening of our designed libraries helped to clarify several sources of simulation error that would have otherwise been difficult to ascertain. Interestingly, the lack of correlation between our simulated and experimentally measured stability values shows clearly that a design procedure need not reproduce experimental data exactly to achieve success. This surprising result suggests potentially fruitful directions for the improvement of computational protein design technology.
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28
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Ahmad SS, Dalby PA. Thermodynamic parameters for salt-induced reversible protein precipitation from automated microscale experiments. Biotechnol Bioeng 2010; 108:322-32. [DOI: 10.1002/bit.22957] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Kumar S. Engineering cytochrome P450 biocatalysts for biotechnology, medicine and bioremediation. Expert Opin Drug Metab Toxicol 2010; 6:115-31. [PMID: 20064075 DOI: 10.1517/17425250903431040] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
IMPORTANCE OF THE FIELD Cytochrome P450 enzymes comprise a superfamily of heme monooxygenases that are of considerable interest for the: i) synthesis of novel drugs and drug metabolites; ii) targeted cancer gene therapy; iii) biosensor design; and iv) bioremediation. However, their applications are limited because cytochrome P450, especially mammalian P450 enzymes, show a low turnover rate and stability, and require a complex source of electrons through cytochrome P450 reductase and NADPH. AREAS COVERED IN THIS REVIEW In this review, we discuss the recent progress towards the use of P450 enzymes in a variety of the above-mentioned applications. We also present alternate and cost-effective ways to perform P450-mediated reaction, especially using peroxides. Furthermore, we expand upon the current progress in P450 engineering approaches describing several recent examples that are utilized to enhance heterologous expression, stability, catalytic efficiency and utilization of alternate oxidants. WHAT THE READER WILL GAIN The review provides a comprehensive knowledge in the design of P450 biocatalysts for potentially practical purposes. Finally, we provide a prospective on the future aspects of P450 engineering and its applications in biotechnology, medicine and bioremediation. TAKE HOME MESSAGE Because of its wide applications, academic and pharmaceutical researchers, environmental scientists and healthcare providers are expected to gain current knowledge and future prospects of the practical use of P450 biocatalysts.
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Affiliation(s)
- Santosh Kumar
- University of Missouri-Kansas City, School of Pharmacy, Division of Pharmacology and Toxicology, 2464 Charlotte St., Kansas City, MO 64108, USA.
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30
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Grant Y, Matejtschuk P, Dalby PA. Rapid optimization of protein freeze-drying formulations using ultra scale-down and factorial design of experiment in microplates. Biotechnol Bioeng 2009; 104:957-64. [PMID: 19530082 DOI: 10.1002/bit.22448] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Retaining biopharmaceutical proteins in a stable form is critical to their safety and efficacy, and is a major factor for optimizing the final product. Freeze-dried formulations offer one route for improved stability. Currently the optimization of formulations for freeze-drying is an empirical process that requires many time-consuming experiments and also uses large quantities of product material. Here we describe a generic framework for the rapid identification and optimization of formulation excipients to prevent loss of protein activity during a lyophilization process. Using factorial design of experiment (DOE) methods combined with lyophilization in microplates a range of optimum formulations were rapidly identified that stabilized lactose dehydrogenase (derived from Lactobacillus leichmanii) during freeze-drying. The procedure outlined herein involves two rounds of factorially designed experiments-an initial screen to identify key excipients and potential interactions followed by a central composite face designed optimization experiment. Polyethylene glycol (PEG) and lactose were shown to have significant effects on maintaining protein stability at the screening stage and optimization resulted in an accurate model that was used to plot a window of operation. The variation of freezing temperatures and rates of sublimation that occur across a microplate during freeze-drying have been characterized also. The optimum formulation was then freeze-dried in stoppered vials to verify that the microscale data was relevant to the effects observed at larger pilot scales. This work provides a generic approach to biopharmaceutical formulation screening where possible excipients can be screened for single and interactive effects thereby increasing throughput while reducing costs in terms of time and materials.
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Affiliation(s)
- Yitzchak Grant
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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31
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Rachinskiy K, Schultze H, Boy M, Bornscheuer U, Büchs J. “Enzyme Test Bench,” a high-throughput enzyme characterization technique including the long-term stability. Biotechnol Bioeng 2009; 103:305-22. [DOI: 10.1002/bit.22242] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Liu PF, Avramova LV, Park C. Revisiting absorbance at 230nm as a protein unfolding probe. Anal Biochem 2009; 389:165-70. [DOI: 10.1016/j.ab.2009.03.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 03/18/2009] [Accepted: 03/19/2009] [Indexed: 11/27/2022]
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33
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34
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Mannall GJ, Myers JP, Liddell J, Titchener-Hooker NJ, Dalby PA. Ultra scale-down of protein refold screening in microwells: Challenges, solutions and application. Biotechnol Bioeng 2009; 103:329-40. [DOI: 10.1002/bit.22245] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Molecular Evolution of Cystine-Stabilized Miniproteins as Stable Proteinaceous Binders. Structure 2009; 17:620-31. [DOI: 10.1016/j.str.2009.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 01/16/2009] [Accepted: 01/16/2009] [Indexed: 11/17/2022]
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36
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Philip AF, Eisenman KT, Papadantonakis GA, Hoff WD. Functional tuning of photoactive yellow protein by active site residue 46. Biochemistry 2009; 47:13800-10. [PMID: 19102703 DOI: 10.1021/bi801730y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-ligand interactions alter the properties of active site groups to achieve specific biological functions. The active site of photoactive yellow protein (PYP) provides a model system for studying such functional tuning. PYP is a small bacterial photoreceptor with photochemistry based on its p-coumaric acid (pCA) chromophore. The absorbance maximum and pK(a) of the pCA in the active site of native PYP are shifted from 400 nm and 8.8 in water to 446 nm and 2.8 in the native protein milieu, respectively, by protein-ligand interactions. We report high-throughput microscale methods for the purification and spectroscopic investigation of PYP and use these to examine the role of active site residue Glu46 in PYP, which is hydrogen bonded to the pCA anion. The functional and structural attributes of the 19 substitution mutants of PYP at critical active site position 46 vary widely, with absorbance maxima from 441 to 478 nm, pCA fluorescence quantum yields from 0.19 to 1.4%, pCA pK(a) values from 3.0 to 9.0, and protein folding stabilities from 6.5 to 12.9 kcal/mol. The kinetics of the last photocycle transition vary by more than 4 orders of magnitude and are often strongly biphasic. Only E46Q PYP exhibits a greatly accelerated photocycling rate. All substitutions yield a folded, photoactive PYP, illustrating the robustness of protein structure and function. Correlations between side chain and mutant properties establish the importance of residue 46 in tuning the function of PYP and the significance of the strength of its hydrogen bond to the pCA. Native PYP exhibits the lowest values for pCA fluorescence quantum yield and pK(a), indicating their functional relevance. These results demonstrate the value of quantitative high-throughput biophysical studies of proteins.
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Affiliation(s)
- Andrew F Philip
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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37
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Garidel P, Hegyi M, Bassarab S, Weichel M. A rapid, sensitive and economical assessment of monoclonal antibody conformational stability by intrinsic tryptophan fluorescence spectroscopy. Biotechnol J 2008; 3:1201-11. [DOI: 10.1002/biot.200800091] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Aucamp JP, Martinez-Torres RJ, Hibbert EG, Dalby PA. A microplate-based evaluation of complex denaturation pathways: Structural stability ofEscherichia coli transketolase. Biotechnol Bioeng 2008; 99:1303-10. [DOI: 10.1002/bit.21705] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Titchener-Hooker NJ, Dunnill P, Hoare M. Micro biochemical engineering to accelerate the design of industrial-scale downstream processes for biopharmaceutical proteins. Biotechnol Bioeng 2008; 100:473-87. [PMID: 18438873 DOI: 10.1002/bit.21788] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- N J Titchener-Hooker
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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40
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Bommarius AS, Broering JM, Chaparro-Riggers JF, Polizzi KM. High-throughput screening for enhanced protein stability. Curr Opin Biotechnol 2006; 17:606-10. [PMID: 17049838 DOI: 10.1016/j.copbio.2006.10.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 08/20/2006] [Accepted: 10/04/2006] [Indexed: 11/17/2022]
Abstract
High thermostability of proteins is a prerequisite for their implementation in biocatalytic processes and in the evolution of new functions. Various protein engineering methods have been applied to the evolution of increased thermostability, including the use of combinatorial design where a diverse library of proteins is generated and screened for variants with increased stability. Current trends are toward the use of data-driven methods that reduce the library size by using available data to choose areas of the protein to target, without specifying the precise changes. For example, the half-lives of subtilisin and a Bacillus subtilis lipase were increased 1500-fold and 300-fold, respectively, using a crystal structure to guide mutagenesis choices. Sequence homology based methods have also produced libraries where 50% of the variants have improved thermostability. Moreover, advances in the high-throughput measurement of denaturation curves and the application of selection methods to thermostability evolution have enabled the screening of larger libraries. The combination of these methods will lead to the rapid improvement of protein stability for biotechnological purposes.
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Affiliation(s)
- Andreas S Bommarius
- School of Chemical & Biomolecular Engineering, 315 Ferst Drive, Georgia Institute of Technology, Atlanta, GA 30332-0363, USA.
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41
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Capelle MAH, Gurny R, Arvinte T. High throughput screening of protein formulation stability: practical considerations. Eur J Pharm Biopharm 2006; 65:131-48. [PMID: 17107777 DOI: 10.1016/j.ejpb.2006.09.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 09/01/2006] [Accepted: 09/18/2006] [Indexed: 11/28/2022]
Abstract
The formulation of protein drugs is a difficult and time-consuming process, mainly due to the complexity of protein structure and the very specific physical and chemical properties involved. Understanding protein degradation pathways is essential for the success of a biopharmaceutical drug. The present review concerns the application of high throughput screening techniques in protein formulation development. A protein high throughput formulation (HTF) platform is based on the use of microplates. Basically, the HTF platform consists of two parts: (i) sample preparation and (ii) sample analysis. Sample preparation involves automated systems for dispensing the drug and the formulation ingredients in both liquid and powder form. The sample analysis involves specific methods developed for each protein to investigate physical and chemical properties of the formulations in microplates. Examples are presented of the use of protein intrinsic fluorescence for the analysis of protein aqueous properties (e.g., conformation and aggregation). Different techniques suitable for HTF analysis are discussed and some of the issues concerning implementation are presented with reference to the use of microplates.
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Affiliation(s)
- Martinus A H Capelle
- Department of Pharmaceutics and Biopharmaceutics, University of Geneva, University of Lausanne, CH-1211 Geneva 4, Switzerland
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42
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Nealon AJ, O’Kennedy RD, Titchener-Hooker NJ, Lye GJ. Quantification and prediction of jet macro-mixing times in static microwell plates. Chem Eng Sci 2006. [DOI: 10.1016/j.ces.2006.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Kumar S, Halpert JR. Use of directed evolution of mammalian cytochromes P450 for investigating the molecular basis of enzyme function and generating novel biocatalysts. Biochem Biophys Res Commun 2005; 338:456-64. [PMID: 16126165 DOI: 10.1016/j.bbrc.2005.08.080] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Indexed: 10/25/2022]
Abstract
Directed evolution has been successfully applied to the design of industrial biocatalysts for enhanced catalytic efficiency and stability, and for examining the molecular basis of enzyme function. Xenobiotic-metabolizing mammalian cytochromes P450 with their catalytic versatility and broad substrate specificity offer the possibility of widespread applications in industrial synthesis, medicine, and bioremediation. However, the requirement for NADPH-cytochrome P450 reductase, often cytochrome b5, and an expensive cofactor, NADPH, complicates the design of mammalian P450 enzymes as biocatalysts. Recently, Guengerich and colleagues have successfully performed directed evolution of P450s 1A2 and 2A6 initially by using colony-based colorimetric and genotoxicity screening assays, respectively, followed by in vitro fluorescence-based activity screening assays. More recently, our laboratory has developed a fluorescence-based in vitro activity screening assay system for enhanced catalytic activity of P450s 2B1 and 3A4. The studies indicate an important role of amino acid residues outside of the active site, which would be difficult to target by other methods. The approach can now be expanded to design these as well as new P450s using more targeted substrates of environmental, industrial, and medical importance.
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Affiliation(s)
- Santosh Kumar
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-1031, USA.
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44
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Abstract
Thermodynamics governs the process of biomolecular recognition. The steps of characterizing, understanding and exploiting binding thermodynamics have the potential to contribute to an improved rational drug design process that is more robust and reliable. It is only relatively recently that instrumentation capable of direct and full thermodynamic characterization has been improved, giving impetus to the application of thermodynamic measurements in drug discovery. This review highlights current instruments and methods that can be employed to measure binding thermodynamics and their use in studies of biomolecular recognition and drug discovery.
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Affiliation(s)
- Geoffrey A Holdgate
- Molecular Enzymology Group, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.
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45
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46
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Hibbert EG, Dalby PA. Directed evolution strategies for improved enzymatic performance. Microb Cell Fact 2005; 4:29. [PMID: 16212665 PMCID: PMC1262762 DOI: 10.1186/1475-2859-4-29] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 10/07/2005] [Indexed: 11/10/2022] Open
Abstract
The engineering of enzymes with altered activity, specificity and stability, using directed evolution techniques that mimic evolution on a laboratory timescale, is now well established. However, the general acceptance of these methods as a route to new biocatalysts for organic synthesis requires further improvement of the methods for both ease-of-use and also for obtaining more significant changes in enzyme properties than is currently possible. Recent advances in library design, and methods of random mutagenesis, combined with new screening and selection tools, continue to push forward the potential of directed evolution. For example, protein engineers are now beginning to apply the vast body of knowledge and understanding of protein structure and function, to the design of focussed directed evolution libraries, with striking results compared to the previously favoured random mutagenesis and recombination of entire genes. Significant progress in computational design techniques which mimic the experimental process of library screening is also now enabling searches of much greater regions of sequence-space for those catalytic reactions that are broadly understood and, therefore, possible to model. Biocatalysis for organic synthesis frequently makes use of whole-cells, in addition to isolated enzymes, either for a single reaction or for transformations via entire metabolic pathways. As many new whole-cell biocatalysts are being developed by metabolic engineering, the potential of directed evolution to improve these initial designs is also beginning to be realised.
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Affiliation(s)
- Edward G Hibbert
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Paul A Dalby
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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