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Xiong Y, Ford NR, Hecht KA, Roesijadi G, Squier TC. Hydrogel Tethering Enhances Interdomain Stabilization of Single-Chain Antibodies. Bioconjug Chem 2017; 28:2804-2814. [DOI: 10.1021/acs.bioconjchem.7b00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yijia Xiong
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
| | - Nicole R. Ford
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Karen A. Hecht
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Guritno Roesijadi
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
- Department
of Microbiology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Thomas C. Squier
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
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2
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Herold EM, John C, Weber B, Kremser S, Eras J, Berner C, Deubler S, Zacharias M, Buchner J. Determinants of the assembly and function of antibody variable domains. Sci Rep 2017; 7:12276. [PMID: 28947772 PMCID: PMC5613017 DOI: 10.1038/s41598-017-12519-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/12/2017] [Indexed: 01/17/2023] Open
Abstract
The antibody Fv module which binds antigen consists of the variable domains VL and VH. These exhibit a conserved ß-sheet structure and comprise highly variable loops (CDRs). Little is known about the contributions of the framework residues and CDRs to their association. We exchanged conserved interface residues as well as CDR loops and tested the effects on two Fvs interacting with moderate affinities (KDs of ~2.5 µM and ~6 µM). While for the rather instable domains, almost all mutations had a negative effect, the more stable domains tolerated a number of mutations of conserved interface residues. Of particular importance for Fv association are VLP44 and VHL45. In general, the exchange of conserved residues in the VL/VH interface did not have uniform effects on domain stability. Furthermore, the effects on association and antigen binding do not strictly correlate. In addition to the interface, the CDRs modulate the variable domain framework to a significant extent as shown by swap experiments. Our study reveals a complex interplay of domain stability, association and antigen binding including an unexpected strong mutual influence of the domain framework and the CDRs on stability/association on the one side and antigen binding on the other side.
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Affiliation(s)
- Eva Maria Herold
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany.,Sanofi-Aventis GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Christine John
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Benedikt Weber
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Stephan Kremser
- Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, 85747, Garching, Germany
| | - Jonathan Eras
- ETH Zürich, Otto-Stern-Weg 5, 8093, Zuerich, Switzerland
| | - Carolin Berner
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Sabrina Deubler
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Martin Zacharias
- Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, 85747, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany.
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3
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Xiong Y, Ford NR, Hecht KA, Roesijadi G, Squier TC. Dynamic Stabilization of Expressed Proteins in Engineered Diatom Biosilica Matrices. Bioconjug Chem 2016; 27:1205-9. [PMID: 27139003 DOI: 10.1021/acs.bioconjchem.6b00165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Self-assembly of recombinant proteins within the biosilica of living diatoms represents a means to construct functional materials in a reproducible and scalable manner that will enable applications that harness the inherent specificities of proteins to sense and respond to environmental cues. Here we describe the use of a silaffin-derived lysine-rich 39-amino-acid targeting sequence (Sil3T8) that directs a single chain fragment variable (scFv) antibody or an enhanced green fluorescent protein (EGFP) to assemble within the biosilica frustule, resulting in abundance of >200 000 proteins per frustule. Using either a fluorescent ligand bound to the scFv or the intrinsic fluorescence of EGFP, we monitored protein conformational dynamics, accessibility to external quenchers, binding affinity, and conformational stability. Like proteins in solution, proteins within isolated frustules undergo isotropic rotational motion, but with 2-fold increases in rotational correlation times that are indicative of weak macromolecular associations within the biosilica. Solvent accessibilities and high-affinity (pM) binding are comparable to those in solution. In contrast to solution conditions, scFv antibodies within the biosilica matrix retain their binding affinity in the presence of chaotropic agents (i.e., 8 M urea). Together, these results argue that dramatic increases in protein conformational stability within the biosilica matrices arise through molecular crowding, acting to retain native protein folds and associated functionality with the potential to allow the utility of engineered proteins under a range of harsh environmental conditions associated with environmental sensing and industrial catalytic transformations.
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Affiliation(s)
- Yijia Xiong
- Department of Basic Medical Sciences, Western University of Health Sciences , Lebanon, Oregon 97355, United States
| | - Nicole R Ford
- Marine Biotechnology Group, Pacific Northwest National Laboratory , Sequim, Washington 98382, United States
| | - Karen A Hecht
- Marine Biotechnology Group, Pacific Northwest National Laboratory , Sequim, Washington 98382, United States
| | - Guritno Roesijadi
- Marine Biotechnology Group, Pacific Northwest National Laboratory , Sequim, Washington 98382, United States.,Department of Microbiology, Oregon State University , Corvallis, Oregon 97331, United States
| | - Thomas C Squier
- Department of Basic Medical Sciences, Western University of Health Sciences , Lebanon, Oregon 97355, United States
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4
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Antibody Binding Selectivity: Alternative Sets of Antigen Residues Entail High-Affinity Recognition. PLoS One 2015; 10:e0143374. [PMID: 26629896 PMCID: PMC4667898 DOI: 10.1371/journal.pone.0143374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/04/2015] [Indexed: 11/19/2022] Open
Abstract
Understanding the relationship between protein sequence and molecular recognition selectivity remains a major challenge. The antibody fragment scFv1F4 recognizes with sub nM affinity a decapeptide (sequence 6TAMFQDPQER15) derived from the N-terminal end of human papilloma virus E6 oncoprotein. Using this decapeptide as antigen, we had previously shown that only the wild type amino-acid or conservative replacements were allowed at positions 9 to 12 and 15 of the peptide, indicating a strong binding selectivity. Nevertheless phenylalanine (F) was equally well tolerated as the wild type glutamine (Q) at position 13, while all other amino acids led to weaker scFv binding. The interfaces of complexes involving either Q or F are expected to diverge, due to the different physico-chemistry of these residues. This would imply that high-affinity binding can be achieved through distinct interfacial geometries. In order to investigate this point, we disrupted the scFv-peptide interface by modifying one or several peptide positions. We then analyzed the effect on binding of amino acid changes at the remaining positions, an altered susceptibility being indicative of an altered role in complex formation. The 23 starting variants analyzed contained replacements whose effects on scFv1F4 binding ranged from minor to drastic. A permutation analysis (effect of replacing each peptide position by all other amino acids except cysteine) was carried out on the 23 variants using the PEPperCHIP® Platform technology. A comparison of their permutation patterns with that of the wild type peptide indicated that starting replacements at position 11, 12 or 13 modified the tolerance to amino-acid changes at the other two positions. The interdependence between the three positions was confirmed by SPR (Biacore® technology). Our data demonstrate that binding selectivity does not preclude the existence of alternative high-affinity recognition modes.
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Vernet T, Choulier L, Nominé Y, Bellard L, Baltzinger M, Travé G, Altschuh D. Spot peptide arrays and SPR measurements: throughput and quantification in antibody selectivity studies. J Mol Recognit 2015; 28:635-44. [PMID: 25960426 DOI: 10.1002/jmr.2477] [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: 12/10/2014] [Revised: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 11/07/2022]
Abstract
Antibody selectivity represents a major issue in the development of efficient immuno-therapeutics and detection assays. Its description requires a comparison of the affinities of the antibody for a significant number of antigen variants. In the case of peptide antigens, this task can now be addressed to a significant level of details owing to improvements in spot peptide array technologies. They allow the high-throughput mutational analysis of peptides with, depending on assay design, an evaluation of binding stabilities. Here, we examine the cross-reactive capacity of an antibody fragment using the PEPperCHIP(®) technology platform (PEPperPRINT GmbH, Heidelberg, Germany; >8800 peptides per microarray) combined with the surface plasmon resonance characterization (Biacore(®) technology; GE-Healthcare Biacore, Uppsala, Sweden) of a subset of interactions. ScFv1F4 recognizes the N-terminal end of oncoprotein E6 of human papilloma virus 16. The spot permutation analysis (i.e. each position substituted by all amino acids except cysteine) of the wild type decapeptide (sequence (6)TAMFQDPQER(15)) and of 15 variants thereof defined the optimal epitope and provided a ranking for variant recognition. The SPR affinity measurements mostly validated the ranking of complex stabilities deduced from array data and defined the sensitivity of spot fluorescence intensities, bringing further insight into the conditions for cross-reactivity. Our data demonstrate the importance of throughput and quantification in the assessment of antibody selectivity.
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Affiliation(s)
- Thierry Vernet
- IBS, Université Grenoble Alpes, F-38044, Grenoble, France.,IBS, CNRS, F-38044, Grenoble, France.,IBS, CEA, F-38044, Grenoble, France
| | - Laurence Choulier
- Biotechnologie et signalisation cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412, Illkirch, France.,Faculté de Pharmacie, CNRS UMR 7213, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France
| | - Yves Nominé
- Biotechnologie et signalisation cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412, Illkirch, France
| | - Laure Bellard
- IBS, Université Grenoble Alpes, F-38044, Grenoble, France.,IBS, CNRS, F-38044, Grenoble, France.,IBS, CEA, F-38044, Grenoble, France
| | - Mireille Baltzinger
- Biotechnologie et signalisation cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412, Illkirch, France.,IBMC, CNRS UPR 9002 - ARN, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg Cedex, France
| | - Gilles Travé
- Biotechnologie et signalisation cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412, Illkirch, France
| | - Danièle Altschuh
- Biotechnologie et signalisation cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412, Illkirch, France
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Engineering venom's toxin-neutralizing antibody fragments and its therapeutic potential. Toxins (Basel) 2014; 6:2541-67. [PMID: 25153256 PMCID: PMC4147596 DOI: 10.3390/toxins6082541] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/16/2014] [Accepted: 08/04/2014] [Indexed: 11/24/2022] Open
Abstract
Serum therapy remains the only specific treatment against envenoming, but anti-venoms are still prepared by fragmentation of polyclonal antibodies isolated from hyper-immunized horse serum. Most of these anti-venoms are considered to be efficient, but their production is tedious, and their use may be associated with adverse effects. Recombinant antibodies and smaller functional units are now emerging as credible alternatives and constitute a source of still unexploited biomolecules capable of neutralizing venoms. This review will be a walk through the technologies that have recently been applied leading to novel antibody formats with better properties in terms of homogeneity, specific activity and possible safety.
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7
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Seeliger D. Development of scoring functions for antibody sequence assessment and optimization. PLoS One 2013; 8:e76909. [PMID: 24204701 PMCID: PMC3804498 DOI: 10.1371/journal.pone.0076909] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/26/2013] [Indexed: 12/27/2022] Open
Abstract
Antibody development is still associated with substantial risks and difficulties as single mutations can radically change molecule properties like thermodynamic stability, solubility or viscosity. Since antibody generation methodologies cannot select and optimize for molecule properties which are important for biotechnological applications, careful sequence analysis and optimization is necessary to develop antibodies that fulfil the ambitious requirements of future drugs. While efforts to grab the physical principles of undesired molecule properties from the very bottom are becoming increasingly powerful, the wealth of publically available antibody sequences provides an alternative way to develop early assessment strategies for antibodies using a statistical approach which is the objective of this paper. Here, publically available sequences were used to develop heuristic potentials for the framework regions of heavy and light chains of antibodies of human and murine origin. The potentials take into account position dependent probabilities of individual amino acids but also conditional probabilities which are inevitable for sequence assessment and optimization. It is shown that the potentials derived from human sequences clearly distinguish between human sequences and sequences from mice and, hence, can be used as a measure of humaness which compares a given sequence with the phenotypic pool of human sequences instead of comparing sequence identities to germline genes. Following this line, it is demonstrated that, using the developed potentials, humanization of an antibody can be described as a simple mathematical optimization problem and that the in-silico generated framework variants closely resemble native sequences in terms of predicted immunogenicity.
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Affiliation(s)
- Daniel Seeliger
- Departement of Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
- * E-mail:
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8
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Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2012; 10:20120835. [PMID: 23235262 PMCID: PMC3565702 DOI: 10.1098/rsif.2012.0835] [Citation(s) in RCA: 274] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.
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Affiliation(s)
- Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Chemistry, Utrecht University, , Padualaan 8, Utrecht, The Netherlands
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9
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Beukes M, Lemmer Y, Deysel M, Al Dulayymi JR, Baird MS, Koza G, Iglesias MM, Rowles RR, Theunissen C, Grooten J, Toschi G, Roberts VV, Pilcher L, Van Wyngaardt S, Mathebula N, Balogun M, Stoltz AC, Verschoor JA. Structure-function relationships of the antigenicity of mycolic acids in tuberculosis patients. Chem Phys Lipids 2010; 163:800-8. [PMID: 20875402 PMCID: PMC3025329 DOI: 10.1016/j.chemphyslip.2010.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/14/2010] [Accepted: 09/17/2010] [Indexed: 11/17/2022]
Abstract
Cell wall mycolic acids (MA) from Mycobacterium tuberculosis (M.tb) are CD1b presented antigens that can be used to detect antibodies as surrogate markers of active TB, even in HIV coinfected patients. The use of the complex mixtures of natural MA is complicated by an apparent antibody cross-reactivity with cholesterol. Here firstly we report three recombinant monoclonal scFv antibody fragments in the chicken germ-line antibody repertoire, which demonstrate the possibilities for cross-reactivity: the first recognized both cholesterol and mycolic acids, the second mycolic acids but not cholesterol, and the third cholesterol but not mycolic acids. Secondly, MA structure is experimentally interrogated to try to understand the cross-reactivity. Unique synthetic mycolic acids representative of the three main functional classes show varying antigenicity against human TB patient sera, depending on the functional groups present and on their stereochemistry. Oxygenated (methoxy- and keto-) mycolic acid was found to be more antigenic than alpha-mycolic acids. Synthetic methoxy-mycolic acids were the most antigenic, one containing a trans-cyclopropane apparently being somewhat more antigenic than the natural mixture. Trans-cyclopropane-containing keto- and hydroxy-mycolic acids were also found to be the most antigenic among each of these classes. However, none of the individual synthetic mycolic acids significantly and reproducibly distinguished the pooled serum of TB positive patients from that of TB negative patients better than the natural mixture of MA. This argues against the potential to improve the specificity of serodiagnosis of TB with a defined single synthetic mycolic acid antigen from this set, although sensitivity may be facilitated by using a synthetic methoxy-mycolic acid.
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Affiliation(s)
- Mervyn Beukes
- Department of Biochemistry, University of Pretoria, South Africa
| | - Yolandy Lemmer
- Department of Biochemistry, University of Pretoria, South Africa
| | - Madrey Deysel
- Department of Biochemistry, University of Pretoria, South Africa
| | | | - Mark S. Baird
- School of Chemistry, University of Wales, Bangor, United Kingdom
| | - Gani Koza
- School of Chemistry, University of Wales, Bangor, United Kingdom
| | | | | | | | - Johan Grooten
- Department of Molecular Biomedical Research, Molecular Immunology Unit, Gent University, Belgium
| | - Gianna Toschi
- Department of Biochemistry, University of Pretoria, South Africa
| | | | - Lynne Pilcher
- Department of Chemistry, University of Pretoria, South Africa
| | | | - Nsovo Mathebula
- Department of Chemistry, University of Pretoria, South Africa
| | | | - Anton C. Stoltz
- Department of Infectious Diseases, University of Pretoria, South Africa
| | - Jan A. Verschoor
- Department of Biochemistry, University of Pretoria, South Africa
- Corresponding author. Tel.: +27 124202477; fax: +27 123625302.
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Kvam E, Sierks MR, Shoemaker CB, Messer A. Physico-chemical determinants of soluble intrabody expression in mammalian cell cytoplasm. Protein Eng Des Sel 2010; 23:489-98. [PMID: 20378699 PMCID: PMC2865363 DOI: 10.1093/protein/gzq022] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 03/02/2010] [Accepted: 03/12/2010] [Indexed: 12/25/2022] Open
Abstract
Soluble antibody fragments are desirable not only as potential therapeutic and diagnostic agents for extracellular targets but also as 'intrabodies' for functional genomics, proteomics and gene therapy inside cells. However, antibody fragments are notoriously aggregation-prone when expressed intracellularly, due in part to unfavorable redox potential and macromolecular crowding in cell cytoplasm. Only a small proportion of intrabodies are soluble in cytoplasm and little is known about the sequence determinants that confer such stability. By comparing the cytoplasmic expression of several related human single-chain variable fragments and camelid V(HH)s in mammalian cells, we report that intrabody solubility is highly influenced by CDR content and is improved by an overall negative charge at cytoplasmic pH and reduced hydrophilicity. We hypothesize that ionic repulsion and weak hydrophobic interactions compensate, to different extents, for impaired disulfide bond formation in cytoplasm, thereby decreasing the risk for intrabody aggregation. As proof of principle, we demonstrate that the soluble expression of an aggregation-prone positively charged intrabody is modestly enhanced via cis or trans acidification using highly charged peptide tags (3XFLAG tag, SV40 NLS). These findings suggest that simple sequence analysis and electrostatic manipulation may aid in predicting and engineering solubility-enhanced intrabodies from antibody libraries for intracellular use.
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Affiliation(s)
- Erik Kvam
- New York State Department of Health, Wadsworth Center/ David Axelrod Institute, 120 New Scotland Ave., PO Box 22002, Albany, NY 12201-2002, USA
- Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Michael R. Sierks
- Department of Chemical Engineering, Arizona State University, Tempe, AZ, USA
| | - Charles B. Shoemaker
- Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Anne Messer
- New York State Department of Health, Wadsworth Center/ David Axelrod Institute, 120 New Scotland Ave., PO Box 22002, Albany, NY 12201-2002, USA
- Department of Biomedical Sciences, University at Albany, Albany, NY, USA
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11
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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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12
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Sibler AP, Baltzinger M, Choulier L, Desplancq D, Altschuh D. SPR identification of mild elution conditions for affinity purification of E6 oncoprotein, using a multivariate experimental design. J Mol Recognit 2008; 21:46-54. [DOI: 10.1002/jmr.865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Baek JH, Im H, Kang UB, Seong KM, Lee C, Kim J, Yu MH. Probing the local conformational change of alpha1-antitrypsin. Protein Sci 2007; 16:1842-50. [PMID: 17660256 PMCID: PMC2206966 DOI: 10.1110/ps.072911607] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The native form of serpins (serine protease inhibitors) is a metastable conformation, which converts into a more stable form upon complex formation with a target protease. It has been suggested that movement of helix-F (hF) and the following loop connecting to strand 3 of beta-sheet A (thFs3A) is critical for such conformational change. Despite many speculations inferred from analysis of the serpin structure itself, direct experimental evidence for the mobilization of hF/thFs3A during the inhibition process is lacking. To probe the mechanistic role of hF and thFs3A during protease inhibition, a disulfide bond was engineered in alpha(1)-antitrypsin, which would lock the displacement of thFs3A from beta-sheet A. We measured the inhibitory activity of each disulfide-locked mutant and its heat stability against loop-sheet polymerization. Presence of a disulfide between thFs3A and s5A but not between thFs3A and s3A caused loss of the inhibitory activity, suggesting that displacement of hF/thFs3A from strand 5A but not from strand 3A is required during the inhibition process. While showing little influence on the inhibitory activity, the disulfide between thFs3A and s3A retarded loop-sheet polymerization significantly. This successful protein engineering of alpha(1)-antitrypsin is expected to be of value in clinical applications. Based on our current studies, we propose that the reactive-site loop of a serpin glides through between s5A and thFs3A for the full insertion into beta-sheet A while a substantial portion of the interactions between hF and s3A is kept intact.
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Affiliation(s)
- Je-Hyun Baek
- Functional Proteomics Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Korea
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14
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Rich RL, Myszka DG. A survey of the year 2002 commercial optical biosensor literature. J Mol Recognit 2004; 16:351-82. [PMID: 14732928 DOI: 10.1002/jmr.649] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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