1
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Fujikawa T, Sasamoto T, Zhao F, Yamagishi A, Akanuma S. Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat. Sci Rep 2024; 14:398. [PMID: 38172176 PMCID: PMC10764835 DOI: 10.1038/s41598-023-50828-4] [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] [Received: 05/22/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One important environmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.
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Affiliation(s)
- Takayuki Fujikawa
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Takahiro Sasamoto
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Fangzheng Zhao
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan.
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2
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Muellers SN, Allen KN, Whitty A. MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability. Proc Natl Acad Sci U S A 2023; 120:e2309884120. [PMID: 38039271 PMCID: PMC10710055 DOI: 10.1073/pnas.2309884120] [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: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal stability based on comparison of the amino acid sequences of homologous proteins derived from bacteria that grow at different temperatures. A key feature of the method is that it compares the sequences based not simply on the amino acid identity, but rather on the structural and physicochemical properties of the side chain. The method accurately identified stabilizing substitutions in three well-studied systems and was validated prospectively by experimentally testing predicted stabilizing substitutions in a polyamine oxidase. In each case, the method outperformed the widely used bioinformatic consensus approach. The method can also provide insight into fundamental aspects of protein structure, for example, by identifying how many sequence positions in a given protein are relevant to temperature adaptation.
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Affiliation(s)
| | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA02215
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA02215
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3
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Thomson RES, Carrera-Pacheco SE, Gillam EMJ. Engineering functional thermostable proteins using ancestral sequence reconstruction. J Biol Chem 2022; 298:102435. [PMID: 36041629 PMCID: PMC9525910 DOI: 10.1016/j.jbc.2022.102435] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
Natural proteins are often only slightly more stable in the native state than the denatured state, and an increase in environmental temperature can easily shift the balance toward unfolding. Therefore, the engineering of proteins to improve protein stability is an area of intensive research. Thermostable proteins are required to withstand industrial process conditions, for increased shelf-life of protein therapeutics, for developing robust 'biobricks' for synthetic biology applications, and for research purposes (e.g., structure determination). In addition, thermostability buffers the often destabilizing effects of mutations introduced to improve other properties. Rational design approaches to engineering thermostability require structural information, but even with advanced computational methods, it is challenging to predict or parameterize all the relevant structural factors with sufficient precision to anticipate the results of a given mutation. Directed evolution is an alternative when structures are unavailable but requires extensive screening of mutant libraries. Recently, however, bioinspired approaches based on phylogenetic analyses have shown great promise. Leveraging the rapid expansion in sequence data and bioinformatic tools, ancestral sequence reconstruction can generate highly stable folds for novel applications in industrial chemistry, medicine, and synthetic biology. This review provides an overview of the factors important for successful inference of thermostable proteins by ancestral sequence reconstruction and what it can reveal about the determinants of stability in proteins.
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Affiliation(s)
- Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Saskya E Carrera-Pacheco
- Centro de Investigación Biomédica (CENBIO), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
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4
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Jia L, Jain M, Sun Y. Improving antibody thermostability based on statistical analysis of sequence and structural consensus data. Antib Ther 2022; 5:202-210. [PMID: 35967906 PMCID: PMC9372885 DOI: 10.1093/abt/tbac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/21/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The use of Monoclonal Antibodies (MAbs) as therapeutics has been increasing over the past 30 years due to their high specificity and strong affinity towards the target. One of the major challenges towarding their use as drugs is their low thermostability, which impacts both efficacy as well as manufacturing and delivery.
Methods
To aid the design of thermally more stable mutants, consensus sequence-based method has been widely used. These methods typically have a success rate of about 50% with maximum melting temperature increment ranging from 10 to 32 °C. In order to improve the prediction performance, we have developed a new and fast MAbs specific method by adding a 3D structural layer to the consensus sequence method. This is done by analyzing the close-by residue pairs which are conserved in more than eight hundred MAbs’ 3D structures.
Results
Combining consensus sequence and structural residue pair covariance methods, we developed an in-house application for predicting human MAb thermostability to guide protein engineers to design stable molecules. Major advantage of this structural level assessment is in significantly reducing the false positives by almost half from the consensus sequence method alone. This application has shown success in designing MAb engineering panels in multiple biologics programs.
Conclusions
Our data science-based method shows impacts in Mab engineering.
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Affiliation(s)
- Lei Jia
- Discovery Research , Amgen, Thousand Oaks, CA, USA
| | - Mani Jain
- Discovery Research , Amgen, Thousand Oaks, CA, USA
| | - Yaxiong Sun
- Discovery Research , Amgen, Thousand Oaks, CA, USA
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5
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Buchholz PCF, van Loo B, Eenink BDG, Bornberg-Bauer E, Pleiss J. Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation. J R Soc Interface 2021; 18:20210389. [PMID: 34727710 DOI: 10.1098/rsif.2021.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolutionary relationships of protein families can be characterized either by networks or by trees. Whereas trees allow for hierarchical grouping and reconstruction of the most likely ancestral sequences, networks lack a time axis but allow for thresholds of pairwise sequence identity to be chosen and, therefore, the clustering of family members with presumably more similar functions. Here, we use the large family of arylsulfatases and phosphonate monoester hydrolases to investigate similarities, strengths and weaknesses in tree and network representations. For varying thresholds of pairwise sequence identity, values of betweenness centrality and clustering coefficients were derived for nodes of the reconstructed ancestors to measure the propensity to act as a bridge in a network. Based on these properties, ancestral protein sequences emerge as bridges in protein sequence networks. Interestingly, many ancestral protein sequences appear close to extant sequences. Therefore, reconstructed ancestor sequences might also be interpreted as yet-to-be-identified homologues. The concept of ancestor reconstruction is compared to consensus sequences, too. It was found that hub sequences in a network, e.g. reconstructed ancestral sequences that are connected to many neighbouring sequences, share closer similarity with derived consensus sequences. Therefore, some reconstructed ancestor sequences can also be interpreted as consensus sequences.
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Affiliation(s)
- Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart 70569, Germany
| | - Bert van Loo
- Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne NE1 8ST, UK.,Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Bernard D G Eenink
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart 70569, Germany
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6
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Akanuma S, Yamaguchi M, Yamagishi A. Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins. PLoS One 2021; 16:e0258821. [PMID: 34673819 PMCID: PMC8530338 DOI: 10.1371/journal.pone.0258821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Further improvement of the thermostability of inherently thermostable proteins is an attractive challenge because more thermostable proteins are industrially more useful and serve as better scaffolds for protein engineering. To establish guidelines that can be applied for the rational design of hyperthermostable proteins, we compared the amino acid sequences of two ancestral nucleoside diphosphate kinases, Arc1 and Bac1, reconstructed in our previous study. Although Bac1 is a thermostable protein whose unfolding temperature is around 100°C, Arc1 is much more thermostable with an unfolding temperature of 114°C. However, only 12 out of 139 amino acids are different between the two sequences. In this study, one or a combination of amino acid(s) in Bac1 was/were substituted by a residue(s) found in Arc1 at the same position(s). The best mutant, which contained three amino acid substitutions (S108D, G116A and L120P substitutions), showed an unfolding temperature more than 10°C higher than that of Bac1. Furthermore, a combination of the other nine amino acid substitutions also led to improved thermostability of Bac1, although the effects of individual substitutions were small. Therefore, not only the sum of the contributions of individual amino acids, but also the synergistic effects of multiple amino acids are deeply involved in the stability of a hyperthermostable protein. Such insights will be helpful for future rational design of hyperthermostable proteins.
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Affiliation(s)
- Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, Tokorozawa, Saitama, Japan
- * E-mail:
| | - Minako Yamaguchi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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7
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Boucher L, Somani S, Negron C, Ma W, Jacobs S, Chan W, Malia T, Obmolova G, Teplyakov A, Gilliland GL, Luo J. Surface salt bridges contribute to the extreme thermal stability of an FN3-like domain from a thermophilic bacterium. Proteins 2021; 90:270-281. [PMID: 34405904 DOI: 10.1002/prot.26218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 03/08/2021] [Accepted: 08/02/2021] [Indexed: 12/27/2022]
Abstract
This study uses differential scanning calorimetry, X-ray crystallography, and molecular dynamics simulations to investigate the structural basis for the high thermal stability (melting temperature 97.5°C) of a FN3-like protein domain from thermophilic bacteria Thermoanaerobacter tengcongensis (FN3tt). FN3tt adopts a typical FN3 fold with a three-stranded beta sheet packing against a four-stranded beta sheet. We identified three solvent exposed arginine residues (R23, R25, and R72), which stabilize the protein through salt bridge interactions with glutamic acid residues on adjacent strands. Alanine mutation of the three arginine residues reduced melting temperature by up to 22°C. Crystal structures of the wild type (WT) and a thermally destabilized (∆Tm -19.7°C) triple mutant (R23L/R25T/R72I) were found to be nearly identical, suggesting that the destabilization is due to interactions of the arginine residues. Molecular dynamics simulations showed that the salt bridge interactions in the WT were stable and provided a dynamical explanation for the cooperativity observed between R23 and R25 based on calorimetry measurements. In addition, folding free energy changes computed using free energy perturbation molecular dynamics simulations showed high correlation with melting temperature changes. This work is another example of surface salt bridges contributing to the enhanced thermal stability of thermophilic proteins. The molecular dynamics simulation methods employed in this study may be broadly useful for in silico surface charge engineering of proteins.
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Affiliation(s)
- Lauren Boucher
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Sandeep Somani
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | - Wenting Ma
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Steven Jacobs
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Winnie Chan
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Thomas Malia
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Galina Obmolova
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Alexey Teplyakov
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Gary L Gilliland
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Jinquan Luo
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
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8
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Mining and Statistical Modeling of Natural and Variant Class IIa Bacteriocins Elucidate Activity and Selectivity Profiles across Species. Appl Environ Microbiol 2020; 86:AEM.01646-20. [PMID: 32917749 DOI: 10.1128/aem.01646-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/08/2020] [Indexed: 12/24/2022] Open
Abstract
Class IIa bacteriocin antimicrobial peptides (AMPs) are a compelling alternative to current antimicrobials because of potential specific activity toward antibiotic-resistant bacteria, including vancomycin-resistant enterococci. Engineering of these molecules would be enhanced by a better understanding of AMP sequence-activity relationships to improve efficacy in vivo and limit effects of off-target activity. Toward this goal, we experimentally evaluated 210 natural and variant class IIa bacteriocins for antimicrobial activity against six strains of enterococci. Inhibitory activity was ridge regressed to AMP sequence to predict performance, achieving an area under the curve of 0.70 and demonstrating the potential of statistical models for identifying and designing AMPs. Active AMPs were individually produced and evaluated against eight enterococcus strains and four Listeria strains to elucidate trends in susceptibility. It was determined that the mannose phosphotransferase system (manPTS) sequence is informative of susceptibility to class IIa bacteriocins, yet other factors, such as membrane composition, also contribute strongly to susceptibility. A broadly potent bacteriocin variant (lactocin DT1) from a Lactobacillus ruminis genome was identified as the only variant with inhibitory activity toward all tested strains, while a novel enterocin variant (DT2) from an Enterococcus faecium genome demonstrated specificity toward Listeria strains. Eight AMPs were evaluated for proteolytic stability to trypsin, chymotrypsin, and pepsin, and three C-terminal disulfide-containing variants, including divercin V41, were identified as compelling for future in vivo studies, given their high potency and proteolytic stability.IMPORTANCE Class IIa bacteriocin antimicrobial peptides (AMPs), an alternative to traditional small-molecule antibiotics, are capable of selective activity toward various Gram-positive bacteria, limiting negative side effects associated with broad-spectrum activity. This selective activity is achieved through targeting of the mannose phosphotransferase system (manPTS) of a subset of Gram-positive bacteria, although factors affecting this mechanism are not entirely understood. Peptides identified from genomic data, as well as variants of previously characterized AMPs, can offer insight into how peptide sequence affects activity and selectivity. The experimental methods presented here identify promising potent and selective bacteriocins for further evaluation, highlight the potential of simple computational modeling for prediction of AMP performance, and demonstrate that factors beyond manPTS sequence affect bacterial susceptibility to class IIa bacteriocins.
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9
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Kang TH, Seong BL. Solubility, Stability, and Avidity of Recombinant Antibody Fragments Expressed in Microorganisms. Front Microbiol 2020; 11:1927. [PMID: 33101218 PMCID: PMC7546209 DOI: 10.3389/fmicb.2020.01927] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Solubility of recombinant proteins (i.e., the extent of soluble versus insoluble expression in heterogeneous hosts) is the first checkpoint criterion for determining recombinant protein quality. However, even soluble proteins often fail to represent functional activity because of the involvement of non-functional, misfolded, soluble aggregates, which compromise recombinant protein quality. Therefore, screening of solubility and folding competence is crucial for improving the quality of recombinant proteins, especially for therapeutic applications. The issue is often highlighted especially in bacterial recombinant hosts, since bacterial cytoplasm does not provide an optimal environment for the folding of target proteins of mammalian origin. Antibody fragments, such as single-chain variable fragment (scFv), single-chain antibody (scAb), and fragment antigen binding (Fab), have been utilized for numerous applications such as diagnostics, research reagents, or therapeutics. Antibody fragments can be efficiently expressed in microorganisms so that they offer several advantages for diagnostic applications such as low cost and high yield. However, scFv and scAb fragments have generally lower stability to thermal stress than full-length antibodies, necessitating a judicious combination of designer antibodies, and bacterial hosts harnessed with robust chaperone function. In this review, we discuss efforts on not only the production of antibodies or antibody fragments in microorganisms but also scFv stabilization via (i) directed evolution of variants with increased stability using display systems, (ii) stabilization of the interface between variable regions of heavy (VH) and light (VL) chains through the introduction of a non-native covalent bond between the two chains, (iii) rational engineering of VH-VL pair, based on the structure, and (iv) computational approaches. We also review recent advances in stability design, increase in avidity by multimerization, and maintaining the functional competence of chimeric proteins prompted by various types of chaperones.
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Affiliation(s)
- Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, South Korea
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10
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Sternke M, Tripp KW, Barrick D. The use of consensus sequence information to engineer stability and activity in proteins. Methods Enzymol 2020; 643:149-179. [PMID: 32896279 DOI: 10.1016/bs.mie.2020.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The goal of protein design is to create proteins that are stable, soluble, and active. Here we focus on one approach to protein design in which sequence information is used to create a "consensus" sequence. Such consensus sequences comprise the most common residue at each position in a multiple sequence alignment (MSA). After describing some general ideas that relate MSA and consensus sequences and presenting a statistical thermodynamic framework that relates consensus and non-consensus sequences to stability, we detail the process of designing a consensus sequence and survey reports of consensus design and characterization from the literature. Many of these consensus proteins retain native biological activities including ligand binding and enzyme activity. Remarkably, in most cases the consensus protein shows significantly higher stability than extant versions of the protein, as measured by thermal or chemical denaturation, consistent with the statistical thermodynamic model. To understand this stability increase, we compare various features of consensus sequences with the extant MSA sequences from which they were derived. Consensus sequences show enrichment in charged residues (most notably glutamate and lysine) and depletion of uncharged polar residues (glutamine, serine, and asparagine). Surprisingly, a survey of stability changes resulting from point substitutions show little correlation with residue frequencies at the corresponding positions within the MSA, suggesting that the high stability of consensus proteins may result from interactions among residue pairs or higher-order clusters. Whatever the source, the large number of reported successes demonstrates that consensus design is a viable route to generating active and in many cases highly stabilized proteins.
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Affiliation(s)
- Matt Sternke
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Katherine W Tripp
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Doug Barrick
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States.
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11
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. Die zentrale Rolle der Methodenentwicklung in der gerichteten Evolution selektiver Enzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201901491] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Deutschland
- Department of Chemistry, Hans-Meerwein-Straße 4 Philipps-Universität 35032 Marburg Deutschland
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12
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Qu G, Li A, Acevedo‐Rocha CG, Sun Z, Reetz MT. The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes. Angew Chem Int Ed Engl 2020; 59:13204-13231. [PMID: 31267627 DOI: 10.1002/anie.201901491] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-resources Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University 368 Youyi Road Wuchang Wuhan 430062 China
| | | | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
- Department of Chemistry, Hans-Meerwein-Strasse 4 Philipps-University 35032 Marburg Germany
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13
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Peng M, Mittmann E, Wenger L, Hubbuch J, Engqvist MKM, Niemeyer CM, Rabe KS. 3D-Printed Phenacrylate Decarboxylase Flow Reactors for the Chemoenzymatic Synthesis of 4-Hydroxystilbene. Chemistry 2019; 25:15998-16001. [PMID: 31618489 PMCID: PMC6972603 DOI: 10.1002/chem.201904206] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/14/2019] [Indexed: 01/24/2023]
Abstract
Continuous flow systems for chemical synthesis are becoming a major focus in organic chemistry and there is a growing interest in the integration of biocatalysts due to their high regio- and stereoselectivity. Methods established for 3D bioprinting enable the fast and simple production of agarose-based modules for biocatalytic reactors if thermally stable enzymes are available. We report here on the characterization of four different cofactor-free phenacrylate decarboxylase enzymes suitable for the production of 4-vinylphenol and test their applicability for the encapsulation and direct 3D printing of disk-shaped agarose-based modules that can be used for compartmentalized flow microreactors. Using the most active and stable phenacrylate decarboxylase from Enterobacter spec. in a setup with four parallel reactors and a subsequent palladium(II) acetate-catalysed Heck reaction, 4-hydroxystilbene was synthesized from p-coumaric acid with a total yield of 14.7 % on a milligram scale. We believe that, due to the convenient direct immobilization of any thermostable enzyme and straightforward tuning of the reaction sequence by stacking of modules with different catalytic activities, this simple process will facilitate the establishment and use of cascade reactions and will therefore be of great advantage for many research approaches.
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Affiliation(s)
- Martin Peng
- Institute for Biological Interfaces (IBG 1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Esther Mittmann
- Institute for Biological Interfaces (IBG 1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Lukas Wenger
- Institute of Functional InterfacesKarlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation EngineeringKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Jürgen Hubbuch
- Institute of Functional InterfacesKarlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation EngineeringKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Martin K. M. Engqvist
- Department of Biology and Biological EngineeringDivision of Systems and Synthetic BiologyChalmers University of TechnologyKemivägen 1041296GothenburgSweden
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Kersten S. Rabe
- Institute for Biological Interfaces (IBG 1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
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14
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Sun W, Yang Z, Lin H, Liu M, Zhao C, Hou X, Hu Z, Cui B. Improvement in affinity and thermostability of a fully human antibody against interleukin-17A by yeast-display technology and CDR grafting. Acta Pharm Sin B 2019; 9:960-972. [PMID: 31649846 PMCID: PMC6804450 DOI: 10.1016/j.apsb.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/24/2018] [Accepted: 11/27/2018] [Indexed: 12/31/2022] Open
Abstract
Monoclonal antibodies (mAbs) are widely used in many fields due to their high specificity and ability to recognize a broad range of antigens. IL-17A can induce a rapid inflammatory response both alone and synergistically with other proinflammatory cytokines. Accumulating evidence suggests that therapeutic intervention of IL-17A signaling offers an attractive treatment option for autoimmune diseases and cancer. Here, we present a combinatorial approach for optimizing the affinity and thermostability of a novel anti-hIL-17A antibody. From a large naïve phage-displayed library, we isolated the anti-IL-17A mAb 7H9 that can neutralize the effects of recombinant human IL-17A. However, the modest neutralization potency and poor thermostability limit its therapeutic applications. In vitro affinity optimization was then used to generate 8D3 by using yeast-displayed random mutagenesis libraries. This resulted in four key amino acid changes and provided an approximately 15-fold potency increase in a cell-based neutralization assay. Complementarity-determining regions (CDRs) of 8D3 were further grafted onto the stable framework of the huFv 4D5 to improve thermostability. The resulting hybrid antibody 9NT/S has superior stabilization and affinities beyond its original antibody. Human fibrosarcoma cell-based assays and in vivo analyses in mice indicated that the anti-IL-17A antibody 9NT/S efficiently inhibited the secretion of IL-17A-induced proinflammatory cytokines. Therefore, this lead anti-IL-17A mAb might be used as a potential best-in-class candidate for treating IL-17A related diseases.
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Key Words
- AIN457, secukinumab
- Antibody engineering
- Antibody maturation
- CDR grafting
- CDRs, complementarity-determining regions
- FACS, fluorescent-activated cell sorting
- HC, heavy chain
- HRP, horse radish peroxidase
- KD, dissociation constant
- Koff, the dissociation rate constant
- Kon, the association rate constant
- LC, light chain
- LY2439821, ixekizumab
- MACS, magnetic-activated cell sorting
- MFI, mean fluorescence intensity
- Monoclonal antibody
- Phage display
- VH, the variable regions of heavy chains
- VL, the variable regions of light chains
- YSD, yeast surface display
- Yeast surface display
- mAbs, monoclonal antibodies
- scFv, single-chain variable fragment
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Affiliation(s)
| | | | | | | | | | | | | | - Bing Cui
- Corresponding author. Tel./fax: +86 10 83165034.
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15
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Wang Q, Chen Y, Park J, Liu X, Hu Y, Wang T, McFarland K, Betenbaugh MJ. Design and Production of Bispecific Antibodies. Antibodies (Basel) 2019; 8:antib8030043. [PMID: 31544849 PMCID: PMC6783844 DOI: 10.3390/antib8030043] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/18/2019] [Accepted: 07/31/2019] [Indexed: 02/07/2023] Open
Abstract
With the current biotherapeutic market dominated by antibody molecules, bispecific antibodies represent a key component of the next-generation of antibody therapy. Bispecific antibodies can target two different antigens at the same time, such as simultaneously binding tumor cell receptors and recruiting cytotoxic immune cells. Structural diversity has been fast-growing in the bispecific antibody field, creating a plethora of novel bispecific antibody scaffolds, which provide great functional variety. Two common formats of bispecific antibodies on the market are the single-chain variable fragment (scFv)-based (no Fc fragment) antibody and the full-length IgG-like asymmetric antibody. Unlike the conventional monoclonal antibodies, great production challenges with respect to the quantity, quality, and stability of bispecific antibodies have hampered their wider clinical application and acceptance. In this review, we focus on these two major bispecific types and describe recent advances in the design, production, and quality of these molecules, which will enable this important class of biologics to reach their therapeutic potential.
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Affiliation(s)
- Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yiqun Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jaeyoung Park
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xiao Liu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yifeng Hu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tiexin Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kevin McFarland
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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16
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 300] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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17
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Cirri E, Brier S, Assal R, Canul-Tec JC, Chamot-Rooke J, Reyes N. Consensus designs and thermal stability determinants of a human glutamate transporter. eLife 2018; 7:40110. [PMID: 30334738 PMCID: PMC6209432 DOI: 10.7554/elife.40110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/17/2018] [Indexed: 11/25/2022] Open
Abstract
Human excitatory amino acid transporters (EAATs) take up the neurotransmitter glutamate in the brain and are essential to maintain excitatory neurotransmission. Our understanding of the EAATs’ molecular mechanisms has been hampered by the lack of stability of purified protein samples for biophysical analyses. Here, we present approaches based on consensus mutagenesis to obtain thermostable EAAT1 variants that share up to ~95% amino acid identity with the wild type transporters, and remain natively folded and functional. Structural analyses of EAAT1 and the consensus designs using hydrogen-deuterium exchange linked to mass spectrometry show that small and highly cooperative unfolding events at the inter-subunit interface rate-limit their thermal denaturation, while the transport domain unfolds at a later stage in the unfolding pathway. Our findings provide structural insights into the kinetic stability of human glutamate transporters, and introduce general approaches to extend the lifetime of human membrane proteins for biophysical analyses.
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Affiliation(s)
- Erica Cirri
- Molecular Mechanisms of Membrane Transport Laboratory, Institut Pasteur, Paris, France.,UMR 3528, CNRS, Institut Pasteur, Paris, France
| | - Sébastien Brier
- Mass Spectrometry for Biology Unit, Institut Pasteur, Paris, France.,USR 2000, CNRS, Institut Pasteur, Paris, France
| | - Reda Assal
- Molecular Mechanisms of Membrane Transport Laboratory, Institut Pasteur, Paris, France.,UMR 3528, CNRS, Institut Pasteur, Paris, France
| | - Juan Carlos Canul-Tec
- Molecular Mechanisms of Membrane Transport Laboratory, Institut Pasteur, Paris, France.,UMR 3528, CNRS, Institut Pasteur, Paris, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, Institut Pasteur, Paris, France.,USR 2000, CNRS, Institut Pasteur, Paris, France
| | - Nicolas Reyes
- Molecular Mechanisms of Membrane Transport Laboratory, Institut Pasteur, Paris, France.,UMR 3528, CNRS, Institut Pasteur, Paris, France
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18
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Stevens AJ, Sekar G, Gramespacher JA, Cowburn D, Muir TW. An Atypical Mechanism of Split Intein Molecular Recognition and Folding. J Am Chem Soc 2018; 140:11791-11799. [PMID: 30156841 PMCID: PMC7232844 DOI: 10.1021/jacs.8b07334] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Split inteins associate to trigger protein splicing in trans, a post-translational modification in which protein sequences fused to the intein pair are ligated together in a traceless manner. Recently, a family of naturally split inteins has been identified that is split at a noncanonical location in the primary sequence. These atypically split inteins show considerable promise in protein engineering applications; however, the mechanism by which they associate is unclear and must be different from that of previously characterized canonically split inteins due to unique topological restrictions. Here, we use a consensus design strategy to generate an atypical split intein pair (Cat) that has greatly improved activity and is amenable to detailed biochemical and biophysical analysis. Guided by the solution structure of Cat, we show that the association of the fragments involves a disorder-to-order structural transition driven by hydrophobic interactions. This molecular recognition mechanism satisfies the topological constraints of the intein fold and, importantly, ensures that premature chemistry does not occur prior to fragment complementation. Our data lead a common blueprint for split intein complementation in which localized structural rearrangements are used to drive folding and regulate protein-splicing activity.
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Affiliation(s)
- Adam J. Stevens
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Josef A. Gramespacher
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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19
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Case BA, Kruziki MA, Johnson SM, Hackel BJ. Engineered Charge Redistribution of Gp2 Proteins through Guided Diversity for Improved PET Imaging of Epidermal Growth Factor Receptor. Bioconjug Chem 2018; 29:1646-1658. [PMID: 29579383 PMCID: PMC6051758 DOI: 10.1021/acs.bioconjchem.8b00144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Gp2 domain is a protein scaffold for synthetic ligand engineering. However, the native protein function results in a heterogeneous distribution of charge on the conserved surface, which may hinder further development and utility. We aim to modulate charge, without diminishing function, which is challenging in small proteins where each mutation is a significant fraction of protein structure. We constructed rationally guided combinatorial libraries with charge-neutralizing or charge-flipping mutations and sorted them, via yeast display and flow cytometry, for stability and target binding. Deep sequencing of functional variants revealed effective mutations both in clone-dependent contexts and broadly across binders to epidermal growth factor receptor (EGFR), insulin receptor, and immunoglobulin G. Functional mutants averaged 4.3 charge neutralizing mutations per domain while maintaining net negative charge. We evolved an EGFR-targeted Gp2 mutant that reduced charge density by 33%, maintained net charge, and improved charge distribution homogeneity while elevating thermal stability ( Tm = 87 ± 1 °C), improving binding specificity, and maintaining affinity ( Kd = 8.8 ± 0.6 nM). This molecule was conjugated with 1,4,7-triazacyclononane,1-glutaric acid-4,7-acetic acid for 64Cu chelation and evaluated for physiological distribution in mice with xenografted A431 (EGFRhigh) and MDA-MB-435 (EGFRlow) tumors. Excised tissue gamma counting and positron emission tomography/computed tomography imaging revealed good EGFRhigh tumor signal (4.7 ± 0.5%ID/g) at 2 h post-injection and molecular specificity evidenced by low uptake in EGFRlow tumors (0.6 ± 0.1%ID/g, significantly lower than for non-charge-modified Gp2, p = 0.01). These results provide charge mutations for an improved Gp2 framework, validate an effective approach to charge engineering, and advance performance of physiological EGFR targeting for molecular imaging.
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Affiliation(s)
- Brett A. Case
- University of Minnesota – Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Max A. Kruziki
- University of Minnesota – Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Sadie M. Johnson
- University of Minnesota – Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Benjamin J. Hackel
- University of Minnesota – Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue SE, Minneapolis, MN 55455
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20
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Maier M, Radtke CP, Hubbuch J, Niemeyer CM, Rabe KS. On-Demand Production of Flow-Reactor Cartridges by 3D Printing of Thermostable Enzymes. Angew Chem Int Ed Engl 2018; 57:5539-5543. [PMID: 29466613 DOI: 10.1002/anie.201711072] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/25/2018] [Indexed: 11/06/2022]
Abstract
The compartmentalization of chemical reactions is an essential principle of life that provides a major source of innovation for the development of novel approaches in biocatalysis. To implement spatially controlled biotransformations, rapid manufacturing methods are needed for the production of biocatalysts that can be applied in flow systems. Whereas three-dimensional (3D) printing techniques offer high-throughput manufacturing capability, they are usually not compatible with the delicate nature of enzymes, which call for physiological processing parameters. We herein demonstrate the utility of thermostable enzymes in the generation of biocatalytic agarose-based inks for a simple temperature-controlled 3D printing process. As examples we utilized an esterase and an alcohol dehydrogenase from thermophilic organisms as well as a decarboxylase that was thermostabilized by directed protein evolution. We used the resulting 3D-printed parts for a continuous, two-step sequential biotransformation in a fluidic setup.
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Affiliation(s)
- Manfred Maier
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Herrmann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Carsten P Radtke
- Karlsruhe Institute of Technology (KIT), Institute for Engineering in Life Science, Section IV: Biomolecular Separation Engineering, Fritz-Haber-Weg 2, 76131, Karlsruhe, Germany
| | - Jürgen Hubbuch
- Karlsruhe Institute of Technology (KIT), Institute for Engineering in Life Science, Section IV: Biomolecular Separation Engineering, Fritz-Haber-Weg 2, 76131, Karlsruhe, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Herrmann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Herrmann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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21
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Maier M, Radtke CP, Hubbuch J, Niemeyer CM, Rabe KS. Herstellung direkt nutzbarer Durchflussreaktorkartuschen durch 3D-Druck von thermostabilen Enzymen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Manfred Maier
- Karlsruher Institut für Technologie (KIT); Institut für Biologische Grenzflächen (IBG 1); Herrmann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Carsten P. Radtke
- Karlsruher Institut für Technologie (KIT); Institut für Bio- und Lebensmitteltechnik, Teilinstitut IV: Molekulare Aufarbeitung von Bioprodukten; Fritz-Haber-Weg 2 76131 Karlsruhe Deutschland
| | - Jürgen Hubbuch
- Karlsruher Institut für Technologie (KIT); Institut für Bio- und Lebensmitteltechnik, Teilinstitut IV: Molekulare Aufarbeitung von Bioprodukten; Fritz-Haber-Weg 2 76131 Karlsruhe Deutschland
| | - Christof M. Niemeyer
- Karlsruher Institut für Technologie (KIT); Institut für Biologische Grenzflächen (IBG 1); Herrmann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Kersten S. Rabe
- Karlsruher Institut für Technologie (KIT); Institut für Biologische Grenzflächen (IBG 1); Herrmann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
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22
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Case BA, Kruziki MA, Stern LA, Hackel BJ. Evaluation of affibody charge modification identified by synthetic consensus design in molecular PET imaging of epidermal growth factor receptor. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2018; 3:171-182. [PMID: 31467687 PMCID: PMC6715147 DOI: 10.1039/c7me00095b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tumor overexpression of epidermal growth factor receptor (EGFR) correlates to therapeutic response in select patient populations. Thus, molecular positron emission tomography (PET) imaging of EGFR could stratify responders versus non-responders. We previously demonstrated effectiveness of a "synthetic consensus" design principle to identify six neutralizing mutations within a 58-amino acid EGFR-targeted affibody domain. Herein, we extend the approach to identify additional neutralized variants that vary net charge from -2 to either -4 or +4 while retaining high affinity (1.6 ± 1.2 nM and 2.5 ± 0.7 nM), specific binding to EGFR, secondary structure, and stability (Tm = 68 °C and 59 °C). We radiolabeled the resultant collection of five charge variants with 64Cu and evaluated PET imaging performance in murine models with subcutaneously xenografted EGFRhigh and EGFRlow tumors. All variants exhibited good EGFRhigh tumor imaging as early as 1 h, with EA35S (+3/-5) achieving 7.7 ± 1.4 %ID/g tumor at 4 h with 1.5 ± 0.3%ID/g EGFRlow tumor, 34 ± 5 tumor:muscle and 12 ± 3 tumor:blood ratios. The positively charged EA62S mutant (+6/-2) exhibited 2.2-3.3-fold higher liver signal than the other variants (p<0.01). The EA68 variant with higher charge density was more stable to human and mouse serum than neutralized variants. In a comparison of radiometal chelators, 1,4,7-triazacyclononane,1-glutaric acid-4,7-acetic acid (NODAGA) exhibited superior physiological specificity to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA). In total, these studies comparatively evaluated a set of EGFR-targeted affibodies varying in net charge and charge density, which revealed functional variations that are useful in engineering an ideal probe for translational studies.
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Affiliation(s)
- Brett A Case
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
| | - Max A Kruziki
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
| | - Lawrence A Stern
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
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Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins. Sci Rep 2018; 8:1227. [PMID: 29352156 PMCID: PMC5775292 DOI: 10.1038/s41598-018-19561-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/03/2018] [Indexed: 11/19/2022] Open
Abstract
Modern organisms commonly use the same set of 20 genetically coded amino acids for protein synthesis with very few exceptions. However, earlier protein synthesis was plausibly much simpler than modern one and utilized only a limited set of amino acids. Nevertheless, few experimental tests of this issue with arbitrarily chosen amino acid sets had been reported prior to this report. Herein we comprehensively and systematically reduced the size of the amino acid set constituting an ancestral nucleoside kinase that was reconstructed in our previous study. We eventually found that two convergent sequences, each comprised of a 13-amino acid alphabet, folded into soluble, stable and catalytically active structures, even though their stabilities and activities were not as high as those of the parent protein. Notably, many but not all of the reduced-set amino acids coincide with those plausibly abundant in primitive Earth. The inconsistent amino acids appeared to be important for catalytic activity but not for stability. Therefore, our findings suggest that the prebiotically abundant amino acids were used for creating stable protein structures and other amino acids with functional side chains were recruited to achieve efficient catalysis.
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24
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Characterization of a thermostable mutant of Agaricus brasiliensis laccase created by phylogeny-based design. J Biosci Bioeng 2017; 124:623-629. [DOI: 10.1016/j.jbiosc.2017.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/28/2017] [Accepted: 07/07/2017] [Indexed: 12/14/2022]
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25
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Akanuma S. Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere. Life (Basel) 2017; 7:life7030033. [PMID: 28783077 PMCID: PMC5617958 DOI: 10.3390/life7030033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 01/02/2023] Open
Abstract
Understanding the evolution of ancestral life, and especially the ability of some organisms to flourish in the variable environments experienced in Earth’s early biosphere, requires knowledge of the characteristics and the environment of these ancestral organisms. Information about early life and environmental conditions has been obtained from fossil records and geological surveys. Recent advances in phylogenetic analysis, and an increasing number of protein sequences available in public databases, have made it possible to infer ancestral protein sequences possessed by ancient organisms. However, the in silico studies that assess the ancestral base content of ribosomal RNAs, the frequency of each amino acid in ancestral proteins, and estimate the environmental temperatures of ancient organisms, show conflicting results. The characterization of ancestral proteins reconstructed in vitro suggests that ancient organisms had very thermally stable proteins, and therefore were thermophilic or hyperthermophilic. Experimental data supports the idea that only thermophilic ancestors survived the catastrophic increase in temperature of the biosphere that was likely associated with meteorite impacts during the early history of Earth. In addition, by expanding the timescale and including more ancestral proteins for reconstruction, it appears as though the Earth’s surface temperature gradually decreased over time, from Archean to present.
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Affiliation(s)
- Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan.
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26
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Medina-Carmona E, Fuchs JE, Gavira JA, Mesa-Torres N, Neira JL, Salido E, Palomino-Morales R, Burgos M, Timson DJ, Pey AL. Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution. Hum Mol Genet 2017; 26:3531-3544. [DOI: 10.1093/hmg/ddx238] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/14/2017] [Indexed: 12/16/2022] Open
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27
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Abstract
BACKGROUND Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have high biotechnological potential. In view of their broad range of applications in research, diagnostics and therapy, engineering their stability is of particular interest. One important aspect is the improvement of thermostability, because it can have immediate effects on conformational stability, protease resistance and aggregation propensity of the protein. METHODS We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data, potentially stabilizing amino acid variations were identified and studied experimentally. RESULTS Some mutations improved the stability of nanobodies by up to 6.1°C, with an average of 2.3°C across eight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stability and aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some instances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasons for this contradiction between prediction and experiment were investigated. CONCLUSIONS The results reveal a mutational strategy to improve the biophysical behavior of nanobody binders and indicate a species-specificity of nanobody architecture. GENERAL SIGNIFICANCE This study illustrates the potential and limitations of engineering nanobody thermostability by merging sequence information with stability data, an aspect that is becoming increasingly important with the recent development of high-throughput biophysical methods.
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28
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Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro' approach to protein engineering. Biochem J 2017; 474:1-19. [PMID: 28008088 DOI: 10.1042/bcj20160507] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 12/22/2022]
Abstract
A central goal in molecular evolution is to understand the ways in which genes and proteins evolve in response to changing environments. In the absence of intact DNA from fossils, ancestral sequence reconstruction (ASR) can be used to infer the evolutionary precursors of extant proteins. To date, ancestral proteins belonging to eubacteria, archaea, yeast and vertebrates have been inferred that have been hypothesized to date from between several million to over 3 billion years ago. ASR has yielded insights into the early history of life on Earth and the evolution of proteins and macromolecular complexes. Recently, however, ASR has developed from a tool for testing hypotheses about protein evolution to a useful means for designing novel proteins. The strength of this approach lies in the ability to infer ancestral sequences encoding proteins that have desirable properties compared with contemporary forms, particularly thermostability and broad substrate range, making them good starting points for laboratory evolution. Developments in technologies for DNA sequencing and synthesis and computational phylogenetic analysis have led to an escalation in the number of ancient proteins resurrected in the last decade and greatly facilitated the use of ASR in the burgeoning field of synthetic biology. However, the primary challenge of ASR remains in accurately inferring ancestral states, despite the uncertainty arising from evolutionary models, incomplete sequences and limited phylogenetic trees. This review will focus, firstly, on the use of ASR to uncover links between sequence and phenotype and, secondly, on the practical application of ASR in protein engineering.
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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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Case BA, Hackel BJ. Synthetic and natural consensus design for engineering charge within an affibody targeting epidermal growth factor receptor. Biotechnol Bioeng 2016; 113:1628-38. [PMID: 26724421 PMCID: PMC5200887 DOI: 10.1002/bit.25931] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 12/19/2015] [Accepted: 12/28/2015] [Indexed: 01/10/2023]
Abstract
Protein ligand charge can impact physiological delivery with charge reduction often benefiting performance. Yet neutralizing mutations can be detrimental to protein function. Herein, three approaches are evaluated to introduce charged-to-neutral mutations of three cations and three anions within an affibody engineered to bind epidermal growth factor receptor. These approaches-combinatorial library sorting or consensus design, based on natural homologs or library-sorted mutants-are used to identify mutations with favorable affinity, stability, and recombinant yield. Consensus design, based on 942 affibody homologs, yielded a mutant of modest function (Kd = 11 ±4 nM, Tm = 62°C, and yield = 4.0 ± 0.8 mg/L as compared to 5.3 ± 1.7 nM, 71°C, and 3.5 ± 0.3 mg/L for the parental affibody). Extension of consensus design to 10 additional mutants exhibited varied performance including a substantially improved mutant (Kd = 6.9 ± 1.4 nM, Tm = 71°C, and 12.7 ± 0.9 mg/L yield). Sorting a homolog-based combinatorial library of 7 × 10(5) mutants generated a distribution of mutants with lower stability and yield, but did identify one strongly binding variant (Kd = 1.2 ± 0.3 nM, Tm = 69°C, and 6.0 ± 0.4 mg/L yield). Synthetic consensus design, based on the amino acid distribution in functional library mutants, yielded higher affinities (P = 0.05) with comparable stabilities and yields. The best of four analyzed clones had Kd = 1.7 ± 0.5 nM, Tm = 68°C, and 7.0 ± 0.5 mg/L yield. While all three approaches were effective in creating targeted affibodies with six charged-to-neutral mutations, synthetic consensus design proved to be the most robust. Synthetic consensus design provides a valuable tool for ligand engineering, particularly in the context of charge manipulation. Biotechnol. Bioeng. 2016;113: 1628-1638. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Brett A Case
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, 356 Amundson Hall, Minneapolis, Minnesota, 55455
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, 356 Amundson Hall, Minneapolis, Minnesota, 55455.
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Itoh N, Kazama M, Takeuchi N, Isotani K, Kurokawa J. Gene-specific amplicons from metagenomes as an alternative to directed evolution for enzyme screening: a case study using phenylacetaldehyde reductases. FEBS Open Bio 2016; 6:566-75. [PMID: 27419059 PMCID: PMC4887972 DOI: 10.1002/2211-5463.12067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/20/2016] [Accepted: 04/05/2016] [Indexed: 02/02/2023] Open
Abstract
Screening gene‐specific amplicons from metagenomes (S‐GAM) is a highly promising technique for the isolation of genes encoding enzymes for biochemical and industrial applications. From metagenomes, we isolated phenylacetaldehyde reductase (par) genes, which code for an enzyme that catalyzes the production of various Prelog's chiral alcohols. Nearly full‐length par genes were amplified by PCR from metagenomic DNA, the products of which were fused with engineered par sequences at both terminal regions of the expression vector to ensure proper expression and then used to construct Escherichia coli plasmid libraries. Sequence‐ and activity‐based screening of these libraries identified different homologous par genes, Hpar‐001 to ‐036, which shared more than 97% amino acid sequence identity with PAR. Comparative characterization of these active homologs revealed a wide variety of enzymatic properties including activity, substrate specificity, and thermal stability. Moreover, amino acid substitutions in these genes coincided with those of Sar268 and Har1 genes, which were independently engineered by error‐prone PCR to exhibit increased activity in the presence of concentrated 2‐propanol. The comparative data from both approaches suggest that sequence information from homologs isolated from metagenomes is quite useful for enzyme engineering. Furthermore, by examining the GAM‐based sequence dataset derived from soil metagenomes, we easily found amino acid substitutions that increase the thermal stability of PAR/PAR homologs. Thus, GAM‐based approaches can provide not only useful homologous enzymes but also an alternative to directed evolution methodologies.
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Affiliation(s)
- Nobuya Itoh
- Biotechnology Research Center and Department of Biotechnology Toyama Prefectural University Imizu Toyama Japan
| | - Miki Kazama
- Biotechnology Research Center and Department of Biotechnology Toyama Prefectural University Imizu Toyama Japan
| | - Nami Takeuchi
- Biotechnology Research Center and Department of Biotechnology Toyama Prefectural University Imizu Toyama Japan
| | - Kentaro Isotani
- Biotechnology Research Center and Department of Biotechnology Toyama Prefectural University Imizu Toyama Japan
| | - Junji Kurokawa
- Biotechnology Research Center and Department of Biotechnology Toyama Prefectural University Imizu Toyama Japan
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Stevens AJ, Brown ZZ, Shah NH, Sekar G, Cowburn D, Muir TW. Design of a Split Intein with Exceptional Protein Splicing Activity. J Am Chem Soc 2016; 138:2162-5. [PMID: 26854538 PMCID: PMC4894280 DOI: 10.1021/jacs.5b13528] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein trans-splicing (PTS) by split inteins has found widespread use in chemical biology and biotechnology. Herein, we describe the use of a consensus design approach to engineer a split intein with enhanced stability and activity that make it more robust than any known PTS system. Using batch mutagenesis, we first conduct a detailed analysis of the difference in splicing rates between the Npu (fast) and Ssp (slow) split inteins of the DnaE family and find that most impactful residues lie on the second shell of the protein, directly adjacent to the active site. These residues are then used to generate an alignment of 73 naturally occurring DnaE inteins that are predicted to be fast. The consensus sequence from this alignment (Cfa) demonstrates both rapid protein splicing and unprecedented thermal and chaotropic stability. Moreover, when fused to various proteins including antibody heavy chains, the N-terminal fragment of Cfa exhibits increased expression levels relative to other N-intein fusions. The durability and efficiency of Cfa should improve current intein based technologies and may provide a platform for the development of new protein chemistry techniques.
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Affiliation(s)
- Adam J Stevens
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Zachary Z Brown
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Neel H Shah
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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Enhancing the thermal tolerance of a cis-epoxysuccinate hydrolase via combining directed evolution with various semi-rational redesign methods. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fukuda Y, Abe A, Tamura T, Kishimoto T, Sogabe A, Akanuma S, Yokobori SI, Yamagishi A, Imada K, Inagaki K. Epistasis effects of multiple ancestral-consensus amino acid substitutions on the thermal stability of glycerol kinase from Cellulomonas sp. NT3060. J Biosci Bioeng 2015; 121:497-502. [PMID: 26493633 DOI: 10.1016/j.jbiosc.2015.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 08/28/2015] [Accepted: 09/16/2015] [Indexed: 10/22/2022]
Abstract
Thermostable variants of the Cellulomonas sp. NT3060 glycerol kinase have been constructed by through the introduction of ancestral-consensus mutations. We produced seven mutants, each having an ancestral-consensus amino acid residue that might be present in the common ancestors of both bacteria and of archaea, and that appeared most frequently at the position of 17 glycerol kinase sequences in the multiple sequence alignment. The thermal stabilities of the resulting mutants were assessed by determining their melting temperatures (Tm), which was defined as the temperature at which 50% of the initial catalytic activity is lost after 15 min of incubation, as well as when the half-life of the catalytic activity occurs at a temperature of 60°C (t1/2). Three mutants showed increased stabilities compared to the wild-type protein. We then produced five more mutants with multiple amino acid substitutions. Some of the resulting mutants showed thermal stabilities much greater than those expected given the stabilities of the respective mutants with single mutations. Therefore, the effects of mutations are not always simply additive and some amino acid substitutions, which do not affect or only slightly improve stability when individually introduced into the protein, show substantial stabilizing effects in combination with other mutations.
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Affiliation(s)
- Yasuhisa Fukuda
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Asuka Abe
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Takashi Tamura
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Takahide Kishimoto
- Biochemical Department, Toyobo Co. Ltd., 2-2-8 Dojima Hama, Kita-ku, Osaka 530-8230, Japan
| | - Atsushi Sogabe
- Biochemical Department, Toyobo Co. Ltd., 2-2-8 Dojima Hama, Kita-ku, Osaka 530-8230, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan
| | - Shin-Ichi Yokobori
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiko Yamagishi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043, Japan
| | - Kenji Inagaki
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
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McConnell AD, Zhang X, Macomber JL, Chau B, Sheffer JC, Rahmanian S, Hare E, Spasojevic V, Horlick RA, King DJ, Bowers PM. A general approach to antibody thermostabilization. MAbs 2015; 6:1274-82. [PMID: 25517312 DOI: 10.4161/mabs.29680] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antibody engineering to enhance thermostability may enable further application and ease of use of antibodies across a number of different areas. A modified human IgG framework has been developed through a combination of engineering approaches, which can be used to stabilize antibodies of diverse specificity. This is achieved through a combination of complementarity-determining region (CDR)-grafting onto the stable framework, mammalian cell display and in vitro somatic hypermutation (SHM). This approach allows both stabilization and maturation to affinities beyond those of the original antibody, as shown by the stabilization of an anti-HA33 antibody by approximately 10°C and affinity maturation of approximately 300-fold over the original antibody. Specificities of 10 antibodies of diverse origin were successfully transferred to the stable framework through CDR-grafting, with 8 of these successfully stabilized, including the therapeutic antibodies adalimumab, stabilized by 9.9°C, denosumab, stabilized by 7°C, cetuximab stabilized by 6.9°C and to a lesser extent trastuzumab stabilized by 0.8°C. This data suggests that this approach may be broadly useful for improving the biophysical characteristics of antibodies across a number of applications.
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Key Words
- CDR, complementarity-determining region
- CH2, heavy chain constant domain 2
- CH3, heavy chain constant domain 3
- DSC, differential scanning calorimetry
- HC, heavy chain
- LC, light chain
- NGF, β-nerve growth factor
- SHM, somatic hypermutation
- SPR, surface plasmon resonance
- TNF, tumor necrosis factor
- Tm, melting temperature
- VH, heavy chain variable region
- VL, light chain variable region
- affinity maturation
- monoclonal antibodies
- protein engineering
- solubility
- somatic hypermutation
- thermostability
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Jacobs SA, Gibbs AC, Conk M, Yi F, Maguire D, Kane C, O'Neil KT. Fusion to a highly stable consensus albumin binding domain allows for tunable pharmacokinetics. Protein Eng Des Sel 2015; 28:385-93. [PMID: 26275855 DOI: 10.1093/protein/gzv040] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/22/2015] [Indexed: 11/14/2022] Open
Abstract
A number of classes of proteins have been engineered for high stability using consensus sequence design methods. Here we describe the engineering of a novel albumin binding domain (ABD) three-helix bundle protein. The resulting engineered ABD molecule, called ABDCon, is expressed at high levels in the soluble fraction of Escherichia coli and is highly stable, with a melting temperature of 81.5°C. ABDCon binds human, monkey and mouse serum albumins with affinity as high as 61 pM. The solution structure of ABDCon is consistent with the three-helix bundle design and epitope mapping studies enabled a precise definition of the albumin binding interface. Fusion of a 10 kDa scaffold protein to ABDCon results in a long terminal half-life of 60 h in mice and 182 h in cynomolgus monkeys. To explore the link between albumin affinity and in vivo exposure, mutations were designed at the albumin binding interface of ABDCon yielding variants that span an 11 000-fold range in affinity. The PK properties of five such variants were determined in mice in order to demonstrate the tunable nature of serum half-life, exposure and clearance with variations in albumin binding affinity.
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Affiliation(s)
- Steven A Jacobs
- Janssen Research & Development, L.L.C., 1400 Welsh & McKean Rd., Spring House, Pennsylvania, PA 19454, USA
| | - Alan C Gibbs
- Janssen Research & Development, L.L.C., 1400 Welsh & McKean Rd., Spring House, Pennsylvania, PA 19454, USA
| | - Michelle Conk
- Janssen Research & Development, L.L.C., 1400 Welsh & McKean Rd., Spring House, Pennsylvania, PA 19454, USA
| | - Fang Yi
- Janssen Research & Development, L.L.C., 1400 Welsh & McKean Rd., Spring House, Pennsylvania, PA 19454, USA
| | - Diane Maguire
- Janssen Research & Development, L.L.C., 1400 Welsh & McKean Rd., Spring House, Pennsylvania, PA 19454, USA
| | - Colleen Kane
- Janssen Research & Development, L.L.C., 1400 Welsh & McKean Rd., Spring House, Pennsylvania, PA 19454, USA
| | - Karyn T O'Neil
- Janssen Research & Development, L.L.C., 1400 Welsh & McKean Rd., Spring House, Pennsylvania, PA 19454, USA
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38
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The consensus-based approach for gene/enzyme replacement therapies and crystallization strategies: the case of human alanine-glyoxylate aminotransferase. Biochem J 2014; 462:453-63. [PMID: 24957194 DOI: 10.1042/bj20140250] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein stability is a fundamental issue in biomedical and biotechnological applications of proteins. Among these applications, gene- and enzyme-replacement strategies are promising approaches to treat inherited diseases that may benefit from protein engineering techniques, even though these beneficial effects have been largely unexplored. In the present study we apply a sequence-alignment statistics procedure (consensus-based approach) to improve the activity and stability of the human AGT (alanine-glyoxylate aminotransferase) protein, an enzyme which causes PH1 (primary hyperoxaluria type I) upon mutation. By combining only five consensus mutations, we obtain a variant (AGT-RHEAM) with largely enhanced in vitro thermal and kinetic stability, increased activity, and with no side effects on foldability and peroxisomal targeting in mammalian cells. The structure of AGT-RHEAM reveals changes at the dimer interface and improved electrostatic interactions responsible for increased kinetic stability. Consensus-based variants maintained the overall protein fold, crystallized more easily and improved the expression as soluble proteins in two different systems [AGT and CIPK24 (CBL-interacting serine/threonine-protein kinase) SOS2 (salt-overly-sensitive 2)]. Thus the consensus-based approach also emerges as a simple and generic strategy to increase the crystallization success for hard-to-get protein targets as well as to enhance protein stability and function for biomedical applications.
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Mesa-Torres N, Salido E, Pey AL. The lower limits for protein stability and foldability in primary hyperoxaluria type I. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2355-65. [PMID: 25461797 DOI: 10.1016/j.bbapap.2014.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/29/2014] [Accepted: 10/10/2014] [Indexed: 01/12/2023]
Abstract
Mutational effects on protein stability and foldability are important to understand conformational diseases and protein evolution. In this work, we perform a comprehensive investigation on the energetic basis underlying mutational effects on the stability of human alanine:glyoxylate aminotransferase (AGT). We study twenty two variants whose kinetic stabilities span over eleven orders of magnitude and are classified into two groups: i) ten naturally-occurring variants, including the most common mutations causing primary hyperoxaluria type I (PH1); and ii) twelve consensus variants obtained by sequence-alignment statistics. We show that AGT dimer stability determines denaturation rates, and mutations modulate stability by changes in the effective thermodynamic stability, the aggregation propensity of partially/globally unfolded states and subtle energetic changes in the rate-limiting denaturation step. In combination with our previous expression analyses in eukaryotic cells, we propose the existence of two lower limits for AGT stability, one linked to optimal folding efficiency (close to the major allele stability) and the other setting a minimal efficiency compatible with glyoxylate detoxification in vivo (close to the minor allele stability). These lower limits could explain the high prevalence of misfolding as a disease mechanism in PH1 and support the use of pharmacological ligands aimed to increase AGT stability as therapies for this disease.
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Affiliation(s)
- Noel Mesa-Torres
- Departamento de Química-Física, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain
| | - Eduardo Salido
- Hospital Universitario de Canarias, Universidad La Laguna, Centre for Biomedical Research on Rare Diseases (CIBERER), Tenerife E-38320, Spain
| | - Angel L Pey
- Departamento de Química-Física, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain.
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40
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Structural basis of the regulatory mechanism of the plant CIPK family of protein kinases controlling ion homeostasis and abiotic stress. Proc Natl Acad Sci U S A 2014; 111:E4532-41. [PMID: 25288725 DOI: 10.1073/pnas.1407610111] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Plant cells have developed specific protective molecular machinery against environmental stresses. The family of CBL-interacting protein kinases (CIPK) and their interacting activators, the calcium sensors calcineurin B-like (CBLs), work together to decode calcium signals elicited by stress situations. The molecular basis of biological activation of CIPKs relies on the calcium-dependent interaction of a self-inhibitory NAF motif with a particular CBL, the phosphorylation of the activation loop by upstream kinases, and the subsequent phosphorylation of the CBL by the CIPK. We present the crystal structures of the NAF-truncated and pseudophosphorylated kinase domains of CIPK23 and CIPK24/SOS2. In addition, we provide biochemical data showing that although CIPK23 is intrinsically inactive and requires an external stimulation, CIPK24/SOS2 displays basal activity. This data correlates well with the observed conformation of the respective activation loops: Although the loop of CIPK23 is folded into a well-ordered structure that blocks the active site access to substrates, the loop of CIPK24/SOS2 protrudes out of the active site and allows catalysis. These structures together with biochemical and biophysical data show that CIPK kinase activity necessarily requires the coordinated releases of the activation loop from the active site and of the NAF motif from the nucleotide-binding site. Taken all together, we postulate the basis for a conserved calcium-dependent NAF-mediated regulation of CIPKs and a variable regulation by upstream kinases.
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41
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Diem MD, Hyun L, Yi F, Hippensteel R, Kuhar E, Lowenstein C, Swift EJ, O'Neil KT, Jacobs SA. Selection of high-affinity Centyrin FN3 domains from a simple library diversified at a combination of strand and loop positions. Protein Eng Des Sel 2014; 27:419-29. [PMID: 24786107 DOI: 10.1093/protein/gzu016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative scaffold molecules represent a class of proteins important to the study of protein design and mechanisms of protein-protein interactions, as well as for the development of therapeutic proteins. Here, we describe the generation of a library built upon the framework of a consensus FN3 domain sequence resulting in binding proteins we call Centyrins. This new library employs diversified positions within the C-strand, CD-loop, F-strand and FG-loop of the FN3 domain. CIS display was used to select high-affinity Centyrin variants against three targets; c-MET, murine IL-17A and rat TNFα and scanning mutagenesis studies were used to define the positions of the library most important for target binding. Contributions from both the strand and loop positions were noted, although the pattern was different for each molecule. In addition, an affinity maturation scheme is described that resulted in a significant improvement in the affinity of one selected Centyrin variant. Together, this work provides important data contributing to our understanding of potential FN3 binding interfaces and a new tool for generating high-affinity scaffold molecules.
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Affiliation(s)
- Michael D Diem
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Linus Hyun
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Fang Yi
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Randi Hippensteel
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Elise Kuhar
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Cassandra Lowenstein
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Edward J Swift
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Karyn T O'Neil
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
| | - Steven A Jacobs
- Janssen Research & Development, L.L.C., 1400 McKean Road, PO Box 776, Spring House, PA 19477, USA
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42
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Hsu HJ, Lee KH, Jian JW, Chang HJ, Yu CM, Lee YC, Chen IC, Peng HP, Wu CY, Huang YF, Shao CY, Chiu KP, Yang AS. Antibody variable domain interface and framework sequence requirements for stability and function by high-throughput experiments. Structure 2013; 22:22-34. [PMID: 24268647 DOI: 10.1016/j.str.2013.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/03/2013] [Accepted: 10/01/2013] [Indexed: 01/21/2023]
Abstract
Protein structural stability and biological functionality are dictated by the formation of intradomain cores and interdomain interfaces, but the intricate sequence-structure-function interrelationships in the packing of protein cores and interfaces remain difficult to elucidate due to the intractability of enumerating all packing possibilities and assessing the consequences of all the variations. In this work, groups of β strand residues of model antibody variable domains were randomized with saturated mutagenesis and the functional variants were selected for high-throughput sequencing and high-throughput thermal stability measurements. The results show that the sequence preferences of the intradomain hydrophobic core residues are strikingly flexible among hydrophobic residues, implying that these residues are coupled indirectly with antigen binding through energetic stabilization of the protein structures. By contrast, the interdomain interface residues are directly coupled with antigen binding. The interdomain interface should be treated as an integral part of the antigen-binding site.
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Affiliation(s)
- Hung-Ju Hsu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuo Hao Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Science, National Taiwan University, Taipei 106, Taiwan; Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program at Academia Sinica, Taipei 115, Taiwan
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chih Yuan Wu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Yun Shao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Zoology, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - An-Suei Yang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
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43
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Abstract
Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature.
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Zidane N, Dussart P, Bremand L, Villani ME, Bedouelle H. Thermodynamic stability of domain III from the envelope protein of flaviviruses and its improvement by molecular design. Protein Eng Des Sel 2013; 26:389-99. [PMID: 23479674 DOI: 10.1093/protein/gzt010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Flavivirus genus includes widespread and severe human pathogens like the four serotypes of dengue virus (DENV1 to DENV4), yellow fever virus, Japanese encephalitis virus and West Nile virus. Domain III (ED3) of the viral envelope protein interacts with cell receptors and contains epitopes recognized by virus neutralizing antibodies. Its structural, antigenic and immunogenic properties have been thoroughly studied contrary to its physico-chemical properties. Here, the ED3 domains of the above pathogenic flaviviruses were produced in the periplasm of Escherichia coli. Their thermodynamic stabilities were measured and compared in experiments of unfolding equilibriums, induced with chemicals or heat and monitored through protein fluorescence. A designed ED3 domain, with the consensus sequence of DENV strains from all serotypes, was highly stable. The low stability of the ED3 domain from DENV3 was increased by three changes of residues in the protein core without affecting its reactivity towards DENV-infected human serums. Additional changes showed that the stability of ED3 varied with the DENV3 genotype. The T(m) of ED3 was higher than 69°C for all the tested viruses and reached 86°C for the consensus ED3. The latter, deprived of its disulfide bond by mutations, was predominantly unfolded at 20°C. These results will help better understand and design the properties of ED3 for its use as diagnostic, vaccine or therapeutic tools.
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Affiliation(s)
- Nora Zidane
- Unit of Molecular Prevention and Therapy of Human Diseases, Department of Infection and Epidemiology, Institut Pasteur, Rue du Dr. Roux, F-75015 Paris, France
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McConnell AD, Spasojevich V, Macomber JL, Krapf IP, Chen A, Sheffer JC, Berkebile A, Horlick RA, Neben S, King DJ, Bowers PM. An integrated approach to extreme thermostabilization and affinity maturation of an antibody. Protein Eng Des Sel 2012; 26:151-64. [DOI: 10.1093/protein/gzs090] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Edwardraja S, Sriram S, Govindan R, Budisa N, Lee SG. Enhancing the thermal stability of a single-chain Fv fragment by in vivo global fluorination of the proline residues. ACTA ACUST UNITED AC 2011; 7:258-65. [DOI: 10.1039/c0mb00154f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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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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Borras L, Gunde T, Tietz J, Bauer U, Hulmann-Cottier V, Grimshaw JPA, Urech DM. Generic approach for the generation of stable humanized single-chain Fv fragments from rabbit monoclonal antibodies. J Biol Chem 2010; 285:9054-66. [PMID: 20056614 DOI: 10.1074/jbc.m109.072876] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite their favorable pharmacokinetic properties, single-chain Fv antibody fragments (scFvs) are not commonly used as therapeutics, mainly due to generally low stabilities and poor production yields. In this work, we describe the identification and optimization of a human scFv scaffold, termed FW1.4, which is suitable for humanization and stabilization of a broad variety of rabbit antibody variable domains. A motif consisting of five structurally relevant framework residues that are highly conserved in rabbit variable domains was introduced into FW1.4 to generate a generically applicable scFv scaffold, termed FW1.4gen. Grafting of complementarity determining regions (CDRs) from 15 different rabbit monoclonal antibodies onto FW1.4 and their derivatives resulted in humanized scFvs with binding affinities in the range from 4.7 x 10(-9) to 1.5 x 10(-11) m. Interestingly, minimalistic grafting of CDRs onto FW1.4gen, without any substitutions in the framework regions, resulted in affinities ranging from 5.7 x 10(-10) to <1.8 x 10(-12) m. When compared with progenitor rabbit scFvs, affinities of most humanized scFvs were similar. Moreover, in contrast to progenitor scFvs, which were difficult to produce, biophysical properties of the humanized scFvs were significantly improved, as exemplified by generally good production yields in a generic refolding process and by apparent melting temperatures between 53 and 86 degrees C. Thus, minimalistic grafting of rabbit CDRs on the FW1.4gen scaffold presents a simple and reproducible approach to humanize and stabilize rabbit variable domains.
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Affiliation(s)
- Leo Borras
- ESBATech, ALCON Biomedical Research Unit, CH-8952 Schlieren, Switzerland
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Wang N, Smith WF, Miller BR, Aivazian D, Lugovskoy AA, Reff ME, Glaser SM, Croner LJ, Demarest SJ. Conserved amino acid networks involved in antibody variable domain interactions. Proteins 2009; 76:99-114. [PMID: 19089973 DOI: 10.1002/prot.22319] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Engineered antibodies are a large and growing class of protein therapeutics comprising both marketed products and many molecules in clinical trials in various disease indications. We investigated naturally conserved networks of amino acids that support antibody V(H) and V(L) function, with the goal of generating information to assist in the engineering of robust antibody or antibody-like therapeutics. We generated a large and diverse sequence alignment of V-class Ig-folds, of which V(H) and V(L) domains are family members. To identify conserved amino acid networks, covariations between residues at all possible position pairs were quantified as correlation coefficients (phi-values). We provide rosters of the key conserved amino acid pairs in antibody V(H) and V(L) domains, for reference and use by the antibody research community. The majority of the most strongly conserved amino acid pairs in V(H) and V(L) are at or adjacent to the V(H)-V(L) interface suggesting that the ability to heterodimerize is a constraining feature of antibody evolution. For the V(H) domain, but not the V(L) domain, residue pairs at the variable-constant domain interface (V(H)-C(H)1 interface) are also strongly conserved. The same network of conserved V(H) positions involved in interactions with both the V(L) and C(H)1 domains is found in camelid V(HH) domains, which have evolved to lack interactions with V(L) and C(H)1 domains in their mature structures; however, the amino acids at these positions are different, reflecting their different function. Overall, the data describe naturally occurring amino acid networks in antibody Fv regions that can be referenced when designing antibodies or antibody-like fragments with the goal of improving their biophysical properties.
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Affiliation(s)
- Norman Wang
- Biogen Idec, San Diego, California 92122, USA
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50
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Bloom JD, Glassman MJ. Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin. PLoS Comput Biol 2009; 5:e1000349. [PMID: 19381264 PMCID: PMC2664478 DOI: 10.1371/journal.pcbi.1000349] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 03/05/2009] [Indexed: 01/08/2023] Open
Abstract
One selection pressure shaping sequence evolution is the requirement that a
protein fold with sufficient stability to perform its biological functions. We
present a conceptual framework that explains how this requirement causes the
probability that a particular amino acid mutation is fixed during evolution to
depend on its effect on protein stability. We mathematically formalize this
framework to develop a Bayesian approach for inferring the stability effects of
individual mutations from homologous protein sequences of known phylogeny. This
approach is able to predict published experimentally measured mutational
stability effects (ΔΔG values) with an accuracy
that exceeds both a state-of-the-art physicochemical modeling program and the
sequence-based consensus approach. As a further test, we use our phylogenetic
inference approach to predict stabilizing mutations to influenza hemagglutinin.
We introduce these mutations into a temperature-sensitive influenza virus with a
defect in its hemagglutinin gene and experimentally demonstrate that some of the
mutations allow the virus to grow at higher temperatures. Our work therefore
describes a powerful new approach for predicting stabilizing mutations that can
be successfully applied even to large, complex proteins such as hemagglutinin.
This approach also makes a mathematical link between phylogenetics and
experimentally measurable protein properties, potentially paving the way for
more accurate analyses of molecular evolution. Mutating a protein frequently causes a change in its stability. As scientists, we
often care about these changes because we would like to engineer a
protein's stability or understand how its stability is impacted by a
naturally occurring mutation. Evolution also cares about mutational stability
changes, because a basic evolutionary requirement is that proteins remain
sufficiently stable to perform their biological functions. Our work is based on
the idea that it should be possible to use the fact that evolution selects for
stability to infer from related proteins the effects of specific mutations. We
show that we can indeed use protein evolutionary histories to computationally
predict previously measured mutational stability changes more accurately than
methods based on either of the two main existing strategies. We then test
whether we can predict mutations that increase the stability of hemagglutinin,
an influenza protein whose rapid evolution is partly responsible for the ability
of this virus to cause yearly epidemics. We experimentally create viruses
carrying predicted stabilizing mutations and find that several do in fact
improve the virus's ability to grow at higher temperatures. Our
computational approach may therefore be of use in understanding the evolution of
this medically important virus.
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Affiliation(s)
- Jesse D Bloom
- Division of Biology, California Institute of Technology, Pasadena, California, USA.
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