Fast antibody fragment motion: flexible linkers act as entropic spring

Stingaciu, Laura R.; Ivanova, Oxana; Ohl, Michael; Biehl, Ralf; Richter, Dieter

doi:10.1038/srep22148

Title: Fast antibody fragment motion: flexible linkers act as entropic spring

Journal Article · Tue Mar 29 00:00:00 EDT 2016 · Scientific Reports

DOI: https://doi.org/10.1038/srep22148 · OSTI ID:1261399

Stingaciu, Laura R. ^[1]; Ivanova, Oxana ^[2]; Ohl, Michael ^[1]; Biehl, Ralf ^[3]; Richter, Dieter ^[4]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Spallation Neutron Source (SNS) and Julich Centre for Neutron Science (JCNS)
Julich Research Centre, Garching (Germany). Julich Centre for Neutron Science (JCNS)
Julich Research Centre and Inst. of Complex Systems, Julich (Germany). Julich Centre for Neutron Science (JCNS)
Julich Research Centre and Inst. of Complex Systems, Julich (Germany). Julich Centre for Neutron Science (JCNS)

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. In conclusion, the Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1261399

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Vol. 6; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (61)

The molecular modeling toolkit: A new approach to molecular simulations Hinsen, Konrad Journal of Computational Chemistry, Vol. 21, Issue 2 https://doi.org/10.1002/(SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B	journal	January 2000
Segmental flexibility in pig immunoglobulin G studied by neutron spin-echo technique Alpert, Yolande; Cser, László; Faragó, Béla Biopolymers, Vol. 24, Issue 9 https://doi.org/10.1002/bip.360240908	journal	September 1985
Small-Angle X-ray Scattering Screening Complements Conventional Biophysical Analysis: Comparative Structural and Biophysical Analysis of Monoclonal Antibodies IgG1, IgG2, and IgG4 Tian, Xinsheng; Langkilde, Annette E.; Thorolfsson, Matthias Journal of Pharmaceutical Sciences, Vol. 103, Issue 6 https://doi.org/10.1002/jps.23964	journal	June 2014
The fab and fc fragments of IgA1 exhibit a different arrangement from that in IgG: a study by X-ray and neutron solution scattering and homology modelling 1 1Edited by R. Huber Boehm, Mark K.; Woof, Jenny M.; Kerr, Michael A. Journal of Molecular Biology, Vol. 286, Issue 5 https://doi.org/10.1006/jmbi.1998.2556	journal	March 1999
Neutron small-angle scattering studies of the general structure of the immunoglobulin G molecule Cser, L.; Gladkikh, I. A.; Kozlov, Zh. A. FEBS Letters, Vol. 68, Issue 2 https://doi.org/10.1016/0014-5793(76)80454-1	journal	October 1976
Electron microscopy of an antibody-hapten complex Valentine, Robin C.; Green, N. Michael Journal of Molecular Biology, Vol. 27, Issue 3 https://doi.org/10.1016/0022-2836(67)90063-0	journal	August 1967
Segmental flexibility in an antibody molecule Yguerabide, Juan; Epstein, Henry F.; Stryer, Lubert Journal of Molecular Biology, Vol. 51, Issue 3 https://doi.org/10.1016/0022-2836(70)90009-4	journal	August 1970
Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 Å and 1.9 Å resolution Marquart, Markus; Deisenhofer, Johann; Huber, Robert Journal of Molecular Biology, Vol. 141, Issue 4 https://doi.org/10.1016/0022-2836(80)90252-1	journal	August 1980
The solution conformations of the subclasses of human IgG deduced from sedimentation and small angle X-ray scattering studies Gregory, L.; Davis, K.; Sheth, B. Molecular Immunology, Vol. 24, Issue 8 https://doi.org/10.1016/0161-5890(87)90184-2	journal	August 1987
Anatomy of the antibody molecule Padlan, Eduardo A. Molecular Immunology, Vol. 31, Issue 3 https://doi.org/10.1016/0161-5890(94)90001-9	journal	February 1994
Many-sphere hydrodynamic interactions and mobilities in a suspension Mazur, P.; van Saarloos, W. Physica A: Statistical Mechanics and its Applications, Vol. 115, Issue 1-2 https://doi.org/10.1016/0378-4371(82)90127-3	journal	September 1982
Self-diffusion of spheres in a concentrated suspension Beenakker, C. W. J.; Mazur, P. Physica A: Statistical Mechanics and its Applications, Vol. 120, Issue 3 https://doi.org/10.1016/0378-4371(83)90061-4	journal	July 1983
Diffusion of spheres in a concentrated suspension II Beenakker, C. W. J.; Mazur, P. Physica A: Statistical Mechanics and its Applications, Vol. 126, Issue 3 https://doi.org/10.1016/0378-4371(84)90206-1	journal	July 1984
Contrasting IgG Structures Reveal Extreme Asymmetry and Flexibility Saphire, Erica Ollmann; Stanfield, Robyn L.; Max Crispin, M. D. Journal of Molecular Biology, Vol. 319, Issue 1 https://doi.org/10.1016/S0022-2836(02)00244-9	journal	May 2002
The role of the inter-heavy chain disulfide bond in modulating the flexibility of immunoglobulin G antibody Chan, L. M.; Cathou, Renata E. Journal of Molecular Biology, Vol. 112, Issue 4 https://doi.org/10.1016/S0022-2836(77)80170-8	journal	June 1977
Harmonicity in slow protein dynamics Hinsen, Konrad; Petrescu, Andrei-Jose; Dellerue, Serge Chemical Physics, Vol. 261, Issue 1-2 https://doi.org/10.1016/S0301-0104(00)00222-6	journal	November 2000
Inelastic neutron scattering from damped collective vibrations of macromolecules Kneller, Gerald R. Chemical Physics, Vol. 261, Issue 1-2 https://doi.org/10.1016/S0301-0104(00)00223-8	journal	November 2000
Myoglobin in crowded solutions: structure and diffusion Longeville, S.; Doster, W.; Kali, G. Chemical Physics, Vol. 292, Issue 2-3 https://doi.org/10.1016/S0301-0104(03)00292-1	journal	August 2003
The study of protein mechanics with the atomic force microscope Fisher, Thomas E.; Oberhauser, Andres F.; Carrion-Vazquez, Mariano Trends in Biochemical Sciences, Vol. 24, Issue 10 https://doi.org/10.1016/S0968-0004(99)01453-X	journal	October 1999
A Rapid Coarse Residue-Based Computational Method for X-Ray Solution Scattering Characterization of Protein Folds and Multiple Conformational States of Large Protein Complexes Yang, Sichun; Park, Sanghyun; Makowski, Lee Biophysical Journal, Vol. 96, Issue 11 https://doi.org/10.1016/j.bpj.2009.03.036	journal	June 2009
Large Domain Fluctuations on 50-ns Timescale Enable Catalytic Activity in Phosphoglycerate Kinase Inoue, R.; Biehl, R.; Rosenkranz, T. Biophysical Journal, Vol. 99, Issue 7 https://doi.org/10.1016/j.bpj.2010.08.017	journal	October 2010
Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models Ortega, A.; Amorós, D.; García de la Torre, J. Biophysical Journal, Vol. 101, Issue 4 https://doi.org/10.1016/j.bpj.2011.06.046	journal	August 2011
The Solution Structure of Rabbit IgG Accounts for Its Interactions with the Fc Receptor and Complement C1q and Its Conformational Stability Rayner, Lucy E.; Kadkhodayi-Kholghi, Nilufar; Heenan, Richard K. Journal of Molecular Biology, Vol. 425, Issue 3 https://doi.org/10.1016/j.jmb.2012.11.019	journal	February 2013
Monomerization of dimeric IgG of intravenous immunoglobulin (IVIg) increases the antibody reactivity against intracellular antigens Wymann, Sandra; Ghielmetti, Marco; Schaub, Alexander Molecular Immunology, Vol. 45, Issue 9 https://doi.org/10.1016/j.molimm.2007.12.020	journal	May 2008
Structure and Flexibility of Individual Immunoglobulin G Molecules in Solution Sandin, Sara; Öfverstedt, Lars-Göran; Wikström, Ann-Charlotte Structure, Vol. 12, Issue 3 https://doi.org/10.1016/j.str.2004.02.011	journal	March 2004
Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-.ANG. resolution Deisenhofer, Johann Biochemistry, Vol. 20, Issue 9 https://doi.org/10.1021/bi00512a001	journal	April 1981
Segmental flexibility of immunoglobulin G antibody molecules in solution: a new interpretation Hanson, Douglas C.; Yguerabide, Juan; Schumaker, Verne N. Biochemistry, Vol. 20, Issue 24 https://doi.org/10.1021/bi00527a016	journal	November 1981
Nanosecond fluorescence spectroscopy of pyrenebutyrate-anti-pyrene antibody complexes Lovejoy, Charles; Holowka, David A.; Cathou, Renata E. Biochemistry, Vol. 16, Issue 16 https://doi.org/10.1021/bi00635a025	journal	August 1977
A Theory of the Structure and Process of Formation of Antibodies ^* Pauling, Linus Journal of the American Chemical Society, Vol. 62, Issue 10 https://doi.org/10.1021/ja01867a018	journal	October 1940
Internal Nanosecond Dynamics in the Intrinsically Disordered Myelin Basic Protein Stadler, Andreas M.; Stingaciu, Laura; Radulescu, Aurel Journal of the American Chemical Society, Vol. 136, Issue 19 https://doi.org/10.1021/ja502343b	journal	May 2014
Intermolecular Interactions of IgG1 Monoclonal Antibodies at High Concentrations Characterized by Light Scattering Scherer, Thomas M.; Liu, Jun; Shire, Steven J. The Journal of Physical Chemistry B, Vol. 114, Issue 40 https://doi.org/10.1021/jp1028646	journal	October 2010
Influence of the Cosolute Environment on IgG Solution Structure Analyzed by Small-Angle X-ray Scattering Lilyestrom, Wayne G.; Shire, Steven J.; Scherer, Thomas M. The Journal of Physical Chemistry B, Vol. 116, Issue 32 https://doi.org/10.1021/jp303839t	journal	August 2012
Immunoglobulin Dynamics, Conformational Fluctuations, and Nonlinear Elasticity and Their Effects on Stability Kamerzell, Tim J.; Ramsey, Joshua D.; Middaugh, C. Russell The Journal of Physical Chemistry B, Vol. 112, Issue 10 https://doi.org/10.1021/jp710061a	journal	March 2008
The rollercoaster ride to anti-cancer antibodies Weiner, Louis M.; Carter, Paul Nature Biotechnology, Vol. 21, Issue 5 https://doi.org/10.1038/nbt0503-510	journal	May 2003
Antibody-targeted radiation cancer therapy Milenic, Diane E.; Brady, Erik D.; Brechbiel, Martin W. Nature Reviews Drug Discovery, Vol. 3, Issue 6 https://doi.org/10.1038/nrd1413	journal	June 2004
Exploring internal protein dynamics by neutron spin echo spectroscopy Biehl, Ralf; Monkenbusch, Michael; Richter, Dieter Soft Matter, Vol. 7, Issue 4 https://doi.org/10.1039/C0SM00683A	journal	January 2011
Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models Kneller, Gerald R. Physical Chemistry Chemical Physics, Vol. 7, Issue 13 https://doi.org/10.1039/b502040a	journal	January 2005
Correlations for interacting Brownian particles Ackerson, Bruce J. The Journal of Chemical Physics, Vol. 64, Issue 1 https://doi.org/10.1063/1.431957	journal	January 1976
Analysis of small angle neutron scattering spectra from polydisperse interacting colloids Kotlarchyk, Michael; Chen, Sow‐Hsin The Journal of Chemical Physics, Vol. 79, Issue 5 https://doi.org/10.1063/1.446055	journal	September 1983
An analytic structure factor for macroion solutions Hayter, John B.; Penfold, Jeff Molecular Physics, Vol. 42, Issue 1 https://doi.org/10.1080/00268978100100091	journal	January 1981
The dynamics of interacting Brownian particles Pusey, P. N. Journal of Physics A: Mathematical and General, Vol. 8, Issue 9 https://doi.org/10.1088/0305-4470/8/9/012	journal	September 1975
Slow internal protein dynamics in solution Biehl, R.; Richter, D. Journal of Physics: Condensed Matter, Vol. 26, Issue 50 https://doi.org/10.1088/0953-8984/26/50/503103	journal	November 2014
Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules Svergun, Dmitri I.; Koch, Michel H. J.; Timmins, Peter A. https://doi.org/10.1093/acprof:oso/9780199639533.001.0001	book	August 2013
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Analysis of Classical Statistical Mechanics by Means of Collective Coordinates Percus, Jerome K.; Yevick, George J. Physical Review, Vol. 110, Issue 1 https://doi.org/10.1103/PhysRev.110.1	journal	April 1958
On the Theory of the Brownian Motion Uhlenbeck, G. E.; Ornstein, L. S. Physical Review, Vol. 36, Issue 5 https://doi.org/10.1103/PhysRev.36.823	journal	September 1930
Effect of rotational diffusion on quasielastic light scattering from fractal colloid aggregates Lindsay, H. M.; Klein, R.; Weitz, D. A. Physical Review A, Vol. 38, Issue 5 https://doi.org/10.1103/PhysRevA.38.2614	journal	September 1988
Rotational diffusion in concentrated colloidal dispersions of hard spheres Degiorgio, Vittorio; Piazza, Roberto; Jones, Robert B. Physical Review E, Vol. 52, Issue 3 https://doi.org/10.1103/PhysRevE.52.2707	journal	September 1995
Exact Solution of the Percus-Yevick Integral Equation for Hard Spheres Wertheim, M. S. Physical Review Letters, Vol. 10, Issue 8 https://doi.org/10.1103/PhysRevLett.10.321	journal	April 1963
Direct Observation of Correlated Interdomain Motion in Alcohol Dehydrogenase Biehl, Ralf; Hoffmann, Bernd; Monkenbusch, Michael Physical Review Letters, Vol. 101, Issue 13 https://doi.org/10.1103/PhysRevLett.101.138102	journal	September 2008
Reentrant Condensation of Proteins in Solution Induced by Multivalent Counterions Zhang, F.; Skoda, M. W. A.; Jacobs, R. M. J. Physical Review Letters, Vol. 101, Issue 14 https://doi.org/10.1103/PhysRevLett.101.148101	journal	September 2008
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis Tirion, Monique M. Physical Review Letters, Vol. 77, Issue 9 https://doi.org/10.1103/PhysRevLett.77.1905	journal	August 1996
On the Theory of the Brownian Motion II Wang, Ming Chen; Uhlenbeck, G. E. Reviews of Modern Physics, Vol. 17, Issue 2-3 https://doi.org/10.1103/RevModPhys.17.323	journal	April 1945
Dirac–Fock calculations of X-ray scattering factors and contributions to the mean inner potential for electron scattering Rez, D.; Rez, P.; Grant, I. Acta Crystallographica Section A Foundations of Crystallography, Vol. 50, Issue 4 https://doi.org/10.1107/S0108767393013200	journal	July 1994
In-depth analysis of subclass-specific conformational preferences of IgG antibodies Tian, Xinsheng; Vestergaard, Bente; Thorolfsson, Matthias IUCrJ, Vol. 2, Issue 1 https://doi.org/10.1107/S205225251402209X	journal	January 2015
Microscopic Diffusion and Hydrodynamic Interactions of Hemoglobin in Red Blood Cells Doster, Wolfgang; Longeville, Stéphane Biophysical Journal, Vol. 93, Issue 4 https://doi.org/10.1529/biophysj.106.097956	journal	August 2007
Emerging Antibody-Based HER2 (ErbB-2/neu) Therapeutics Krauss, W. C.; Park, J. W.; Kirpotin, D. B. Breast Disease, Vol. 11, Issue 1 https://doi.org/10.3233/BD-1999-11110	journal	June 2000
IgG Subclasses and Allotypes: From Structure to Effector Functions Vidarsson, Gestur; Dekkers, Gillian; Rispens, Theo Frontiers in Immunology, Vol. 5 https://doi.org/10.3389/fimmu.2014.00520	journal	October 2014
Stability of IgG isotypes in serum Correia, Ivan mAbs, Vol. 2, Issue 3 https://doi.org/10.4161/mabs.2.3.11788	journal	May 2010
Structural analysis of a therapeutic monoclonal antibody dimer by hydroxyl radical footprinting Deperalta, Galahad; Alvarez, Melissa; Bechtel, Charity mAbs, Vol. 5, Issue 1 https://doi.org/10.4161/mabs.22964	journal	January 2013
Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations Kortkhonjia, Ekaterine; Brandman, Relly; Zhou, Joe Zhongxiang mAbs, Vol. 5, Issue 2 https://doi.org/10.4161/mabs.23651	journal	March 2013

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