Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules
Jacob L. Jordan
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904
The first two authors contributed equally to this work.
Search for more papers by this authorJoseph W. Arndt
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
The first two authors contributed equally to this work.
Search for more papers by this authorKarl Hanf
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Search for more papers by this authorGuohui Li
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Search for more papers by this authorJanine Hall
Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904
Search for more papers by this authorStephen Demarest
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorFlora Huang
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorXiufeng Wu
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorBrian Miller
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorScott Glaser
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorErik J. Fernandez
Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904
Search for more papers by this authorCorresponding Author
Deping Wang
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, MA 02142===Search for more papers by this authorCorresponding Author
Alexey Lugovskoy
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, MA 02142===Search for more papers by this authorJacob L. Jordan
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904
The first two authors contributed equally to this work.
Search for more papers by this authorJoseph W. Arndt
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
The first two authors contributed equally to this work.
Search for more papers by this authorKarl Hanf
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Search for more papers by this authorGuohui Li
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Search for more papers by this authorJanine Hall
Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904
Search for more papers by this authorStephen Demarest
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorFlora Huang
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorXiufeng Wu
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorBrian Miller
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorScott Glaser
Biogen Idec, Inc., 5200 Research Place, San Diego, California 92122
Search for more papers by this authorErik J. Fernandez
Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904
Search for more papers by this authorCorresponding Author
Deping Wang
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, MA 02142===Search for more papers by this authorCorresponding Author
Alexey Lugovskoy
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142
Biogen Idec, Inc., 12 Cambridge Center, Cambridge, MA 02142===Search for more papers by this authorAbstract
Bispecific immunoglobulin-like antibodies capable of engaging multiple antigens represent a promising new class of therapeutic agents. Engineering of these molecules requires optimization of the molecular properties of one of the domain components. Here, we present a detailed crystallographic and computational characterization of the stabilization patterns in the lymphotoxin-beta receptor (LTβR) binding Fv domain of an anti-LTβR/anti-TNF-related apoptosis inducing ligand receptor-2 (TRAIL-R2) bispecific immunoglobulin-like antibody. We further describe a new hierarchical structure-guided approach toward engineering of antibody-like molecules to enhance their thermal and chemical stability. Proteins 2009. © 2009 Wiley-Liss, Inc.
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REFERENCES
- 1 Cleland JL,Lam X,Kendrick B,Yang J,Yang T-H,Overcashier D,Brooks D,Hsu C,Carpenter JF. A specific molar ratio of stabilizer to protein is required for storage stability of a lyophilized monoclonal antibody. J Pharm Sci 2001; 90: 310–321.
- 2 Roberts CJ. Non-native protein aggregation kinetics. Biotech Bioeng 2007; 98: 927–938.
- 3 Holliger P,Hudson PJ. Engineered antibody fragments and the rise of single domains. Nature Biotech 2005; 23: 1126–1136.
- 4 Neylon C. Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucl Acids Res 2004; 32: 1448–1459.
- 5 Eijsink VGH,Gåseidnes S,Borchert TV,van den Burg B. Directed evolution of enzyme stability. Biomol Eng 2005; 22: 21–30.
- 6 Bolon DN,Mayo SL. Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 2001; 98: 14274–14279.
- 7 Michaelson JS,Demarest SJ,Miller B,Amatucci A,Hughes I,Snyder WB,Wu X,Huang F,Phan S,Gao S,Doern A,Lugovskoy A,Joseph I,Bailly V,Wang X,Garber E,Browning J,Glaser SM. Anti-tumor activity of stability-engineered IgG like bispecific antibodies targeting TRAIL-R2 AND LTBetaR. Monocolonal Antibodies 2009; 1: 128–141.
- 8 Honneger A. Engineering antibodies for stability and efficient folding. Handb Exp Pharmacol 2008; 181: 47–68.
- 9 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.
- 10 Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14: 755–763.
- 11 Demarest SJ,Rogers J,Hansen G. Optimization of the antibody C(H)3 domain by residue frequency analysis of IgG sequences. J Mol Biol 2004; 335: 41–48.
- 12 Chothia C,Gelfand I,Kister A. Structural determinants in the sequences of immunoglobulin variable domain. J Mol Bio 1998; 278: 457–479.
- 13 Desmet J,De Maeyer M,Hazes B,Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992; 356: 539–542.
- 14 Lasters I,Desmet J. The fuzzy-end elimination theorem: correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem. Protein Eng 1993; 6: 717–722.
- 15 Goldstein RF. Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J 1994; 66: 1335–1340.
- 16 Pace CN. Contribution of the hydrophobic effect to globular protein stability. J Mol Biol 1992; 226: 29–35.
- 17 Pierce NA,Spriet JA,Desmet J,Mayo SL. Conformational splitting: a more powerful criterion for dead-end elimination. J Comp Chem 2000; 21: 999–1009.
- 18 Hanf KJM. Protein Design with Hierarchical Treatment of Solvation and Electrostatics. Thesis, Massachusetts Institute of Technology, Cambridge, MA 2002.
- 19
Mendes J,Baptista AM,Carrondo MA,Soares CM.
Improved modeling of side-chains in proteins with rotamer-based methods: a flexible rotamer model.
Proteins
1999;
37:
530–543.
10.1002/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H CAS PubMed Web of Science® Google Scholar
- 20 Caravella JA. Electrostatics and packing in biomolecules: accounting for conformational change in protein folding and binding. Thesis, Cambridge, MA: Massachusetts Institute of Technology; 2002.
- 21 Dunbrack RL,Jr,Karplus M. Backbone-dependent rotamer library for proteins: application to side-chain prediction. J Mol Biol 1993; 230: 543–574.
- 22 Gilson MK,Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature 1987; 330: 84–86.
- 23 Gilson MK,Sharp KA,Honig BH. Calculating the electrostatic potential of molecules in solution: method and error assessment. JComp Chem 1988; 9: 327–335.
- 24 Sharp KA,Honig BH. Electrostatic interactions in macromolecules: theory and applications. Annu Rev Biophys Bio 1990; 19: 301–332.
- 25 Gordon DB,Mayo SL. Branch-and terminate: a combinatorial optimization algorithm for protein design. Structure 1999; 7: 1089–1098.
- 26 Brooks BR,Bruccoleri RE,Olafson BD,States DJ,Swaminathan S,Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983; 4: 187–217.
- 27 Kortemme T,Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002; 9: 14116–14121.
- 28 Kuhlman B,O'Neill JW,Kim DE,Zhang KY,Baker D. Conversion of monomeric protein L to an obligate dimer by computational protein design. Proc Natl Acad Sci USA 2001; 98: 10687–10691.
- 29 Sali A,Blundell TL. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779–815.
- 30 Canutescu AA,Shelenkov AA,Dunbrack RL,Jr. A graph-theory algorithm for rapid protein side-chain prediction. Prot Sci 1993; 12: 2001–2014.
- 31 Miller BR,Glaser SM,Demarest SJ. Rapid screening platform for stabilization of scFvs in Escherichia coli. Methods Mol Bio 2009; 525: 1–11.
- 32 Vagin A,Teplyakov A. MOLREP: an automated program for molecular replacement. J Appl Crystallogr 1997; 30: 1022–1025.
- 33 Emsley P,Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallographica 2004; D60: 2126–2132.
- 34
Collaborative Computational Project Number 4.
“The CCP4 Suite: Programs for Protein Crystallography”.
Acta Crystallogr D Biol Crystallographica
1994;
D50:
760–763.
10.1107/S0907444994003112 Google Scholar
- 35 Davis IW,Murray LW,Richardson JS,Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucl Acids Res 2004; 32: W615–W619.
- 36 Dantas G,Kuhlman B,Callender D,Wong M,Baker D. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 2003; 332: 449–460.
- 37 Kuhlman B,Dantas G,Ireton GC,Varani G,Stoddard BL,Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003; 302: 1364–1368.
- 38
Lazaridis T,Karplus M.
Effective energy function for proteins in solution.
Proteins
1999;
35:
133–152.
10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N CAS PubMed Web of Science® Google Scholar
- 39 Kortemme T,Morozov AV,Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003; 326: 1239–1259.
- 40 Dunbrack RL,Jr,Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Prot Sci 1997; 6: 1661–1681.
- 41 Dantas G,Corrent C,Reichow SL,Havranek JJ,Eletr ZM,Isern NG,Kuhlman B,Varani G,Merritt EA,Baker D. High-resolution structural and thermodynamic analysis of extreme stabilization of procarboxypeptidase by computational protein design. J Mol Biol 2007; 366: 1209–1221.
- 42 Myers JK,Pace CN,Scholtz JM. Denaturant m values and heat capacity changes: relation to changes in accessible surfaces areas of protein unfolding. Prot Sci 1995; 4: 2138–2148.
- 43 Röthlisberger D,Honegger A,Plückthun A. Domain interactions in the Fab fragment: a comparative evaluation of the single-chain Fv and Fab format engineered with variable domains of different stability. J Mol Biol 2005; 347: 773–789.
- 44 Willard L,Ranjan A,Zhang H,Monzavi H,Boyko RF,Sykes BD,Wishart DS. VADAR: a web server for quantitative evaluation of protein structure quality. Nucl Acids Res 2003; 31: 3316–3319.
- 45 Simons KT,Kooperberg C,Huang E,Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268: 209–225.
- 46
Simons KT,Ruczinski I,Kooperberg C,Fox BA,Bystroff C,Baker D.
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins.
Proteins
1999;
34:
82–95.
10.1002/(SICI)1097-0134(19990101)34:1<82::AID-PROT7>3.0.CO;2-A CAS PubMed Web of Science® Google Scholar
- 47 Sammond DW,Eletr ZM,Purbeck C,Kimple RJ,Siderovski DP,Kuhlman B. Structure-based protocol for identifying mutations that enhance protein-protein binding affinities. J Mol Biol 2007; 371: 1392–1404.
- 48 Ishikawa K,Nakamura H,Morikawa K,Kanaya S. Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core. Biochemistry 1993; 32: 6171–6178.