The role of complementary shape in protein dimerization
Abstract
Shape guides colloidal nanoparticles to form complex assemblies, but its role in defining interfaces in biomolecular complexes is less clear. In this work, we isolate the role of shape in protein complexes by studying the reversible binding processes of 46 protein dimer pairs, and investigate when entropic effects from shape complementarity alone are sufficient to predict the native protein binding interface. We employ depletants using a generic, implicit depletion model to amplify the magnitude of the entropic forces arising from lock-and-key binding and isolate the effect of shape complementarity in protein dimerization. For 13% of the complexes studied here, protein shape is sufficient to predict native complexes as equilibrium assemblies. We elucidate the results by analyzing the importance of competing binding configurations and how it affects the assembly. Furthermore, a machine learning classifier, with a precision of 89.14% and a recall of 77.11%, is able to identify the cases where shape alone predicts the native protein interface.
- Authors:
-
- Univ. of Michigan, Ann Arbor, MI (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1818678
- Alternate Identifier(s):
- OSTI ID: 1810181
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Soft Matter
- Additional Journal Information:
- Journal Volume: 17; Journal Issue: 31; Journal ID: ISSN 1744-683X
- Publisher:
- Royal Society of Chemistry
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE
Citation Formats
Gao, Fengyi, Glaser, Jens, and Glotzer, Sharon C. The role of complementary shape in protein dimerization. United States: N. p., 2021.
Web. doi:10.1039/d1sm00468a.
Gao, Fengyi, Glaser, Jens, & Glotzer, Sharon C. The role of complementary shape in protein dimerization. United States. https://doi.org/10.1039/d1sm00468a
Gao, Fengyi, Glaser, Jens, and Glotzer, Sharon C. Mon .
"The role of complementary shape in protein dimerization". United States. https://doi.org/10.1039/d1sm00468a. https://www.osti.gov/servlets/purl/1818678.
@article{osti_1818678,
title = {The role of complementary shape in protein dimerization},
author = {Gao, Fengyi and Glaser, Jens and Glotzer, Sharon C.},
abstractNote = {Shape guides colloidal nanoparticles to form complex assemblies, but its role in defining interfaces in biomolecular complexes is less clear. In this work, we isolate the role of shape in protein complexes by studying the reversible binding processes of 46 protein dimer pairs, and investigate when entropic effects from shape complementarity alone are sufficient to predict the native protein binding interface. We employ depletants using a generic, implicit depletion model to amplify the magnitude of the entropic forces arising from lock-and-key binding and isolate the effect of shape complementarity in protein dimerization. For 13% of the complexes studied here, protein shape is sufficient to predict native complexes as equilibrium assemblies. We elucidate the results by analyzing the importance of competing binding configurations and how it affects the assembly. Furthermore, a machine learning classifier, with a precision of 89.14% and a recall of 77.11%, is able to identify the cases where shape alone predicts the native protein interface.},
doi = {10.1039/d1sm00468a},
journal = {Soft Matter},
number = 31,
volume = 17,
place = {United States},
year = {Mon Jul 19 00:00:00 EDT 2021},
month = {Mon Jul 19 00:00:00 EDT 2021}
}
Works referenced in this record:
cGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein–DNA ladders
journal, September 2017
- Andreeva, Liudmila; Hiller, Björn; Kostrewa, Dirk
- Nature, Vol. 549, Issue 7672
Shape Complementarity at Protein/Protein Interfaces
journal, December 1993
- Lawrence, Michael C.; Colman, Peter M.
- Journal of Molecular Biology, Vol. 234, Issue 4
Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking
journal, April 2016
- Kuroda, Daisuke; Gray, Jeffrey J.
- Bioinformatics, Vol. 32, Issue 16
Computational prediction of protein interfaces: A review of data driven methods
journal, October 2015
- Xue, Li C.; Dobbs, Drena; Bonvin, Alexandre M. J. J.
- FEBS Letters, Vol. 589, Issue 23
Dockground: A comprehensive data resource for modeling of protein complexes
journal, October 2017
- Kundrotas, Petras J.; Anishchenko, Ivan; Dauzhenka, Taras
- Protein Science, Vol. 27, Issue 1
A novel shape complementarity scoring function for protein-protein docking
journal, May 2003
- Chen, Rong; Weng, Zhiping
- Proteins: Structure, Function, and Genetics, Vol. 51, Issue 3
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
journal, December 2019
- Gainza, P.; Sverrisson, F.; Monti, F.
- Nature Methods, Vol. 17, Issue 2
Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments
journal, February 2001
- Padilla, J. E.; Colovos, C.; Yeates, T. O.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 5
Morphometric Approach to Many-Body Correlations in Hard Spheres
journal, February 2019
- Robinson, Joshua F.; Turci, Francesco; Roth, Roland
- Physical Review Letters, Vol. 122, Issue 6
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
journal, May 2012
- King, N. P.; Sheffler, W.; Sawaya, M. R.
- Science, Vol. 336, Issue 6085
Constructing protein polyhedra via orthogonal chemical interactions
journal, January 2020
- Golub, Eyal; Subramanian, Rohit H.; Esselborn, Julian
- Nature, Vol. 578, Issue 7793
The packing of α-helices: simple coiled-coils
journal, September 1953
- Crick, F. H. C.
- Acta Crystallographica, Vol. 6, Issue 8
Einfluss der Configuration auf die Wirkung der Enzyme
journal, October 1894
- Fischer, Emil
- Berichte der deutschen chemischen Gesellschaft, Vol. 27, Issue 3
Supraparticle Nanoassemblies with Enzymes
journal, August 2019
- de Q. Silveira, Gleiciani; Ramesar, Naomi S.; Nguyen, Trung Dac
- Chemistry of Materials, Vol. 31, Issue 18
Shape complementarity at the hemoglobin ?1?1 subunit interface
journal, July 1986
- Connolly, Michael L.
- Biopolymers, Vol. 25, Issue 7
PrP c capping in T cells promotes its association with the lipid raft proteins reggie‐1 and reggie‐2 and leads to signal transduction
journal, September 2004
- Stuermer, Claudia A. O.; Langhorst, Matthias F.; Wiechers, Marianne F.
- The FASEB Journal, Vol. 18, Issue 14
Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase
journal, July 2011
- Cardinale, D.; Guaitoli, G.; Tondi, D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 34
The Key–Lock Theory and the Induced Fit Theory
journal, January 1995
- Koshland, Daniel E.
- Angewandte Chemie International Edition in English, Vol. 33, Issue 2324
Control of Pathways and Yields of Protein Crystallization through the Interplay of Nonspecific and Specific Attractions
journal, August 2010
- Whitelam, Stephen
- Physical Review Letters, Vol. 105, Issue 8
Lock and key colloids
journal, March 2010
- Sacanna, S.; Irvine, W. T. M.; Chaikin, P. M.
- Nature, Vol. 464, Issue 7288
Spatial distribution of a depletion potential between a big solute of arbitrary geometry and a big sphere immersed in small spheres
journal, February 2002
- Kinoshita, Masahiro
- The Journal of Chemical Physics, Vol. 116, Issue 8
Lock and key model system
journal, December 2008
- König, P. -M.; Roth, R.; Dietrich, S.
- EPL (Europhysics Letters), Vol. 84, Issue 6
XSEDE: Accelerating Scientific Discovery
journal, September 2014
- Towns, John; Cockerill, Timothy; Dahan, Maytal
- Computing in Science & Engineering, Vol. 16, Issue 5
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment
journal, June 2016
- Lensink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy
- Proteins: Structure, Function, and Bioinformatics, Vol. 84, Issue S1
An ultra-stable gold-coordinated protein cage displaying reversible assembly
journal, May 2019
- Malay, Ali D.; Miyazaki, Naoyuki; Biela, Artur
- Nature, Vol. 569, Issue 7756
Exaptation of two ancient immune proteins into a new dimeric pore-forming toxin in snails
journal, August 2020
- Giglio, M. L.; Ituarte, S.; Milesi, V.
- Journal of Structural Biology, Vol. 211, Issue 2
Using depletion to control colloidal crystal assemblies of hard cuboctahedra
journal, January 2016
- Karas, Andrew S.; Glaser, Jens; Glotzer, Sharon C.
- Soft Matter, Vol. 12, Issue 23
Reduced surface: An efficient way to compute molecular surfaces
journal, March 1996
- Sanner, Michel F.; Olson, Arthur J.; Spehner, Jean-Claude
- Biopolymers, Vol. 38, Issue 3
Spiers Memorial Lecture: Effect of interaction specificity on the phase behaviour of patchy particles
journal, January 2012
- Dorsaz, Nicolas; Filion, Laura; Smallenburg, Frank
- Faraday Discussions, Vol. 159
freud: A software suite for high throughput analysis of particle simulation data
journal, September 2020
- Ramasubramani, Vyas; Dice, Bradley D.; Harper, Eric S.
- Computer Physics Communications, Vol. 254
On Interaction between Two Bodies Immersed in a Solution of Macromolecules
journal, July 1954
- Asakura, Sho; Oosawa, Fumio
- The Journal of Chemical Physics, Vol. 22, Issue 7
Protein-Protein Docking: From Interaction to Interactome
journal, October 2014
- Vakser, Ilya A.
- Biophysical Journal, Vol. 107, Issue 8
Crystallization of asymmetric patchy models for globular proteins in solution
journal, July 2013
- Fusco, Diana; Charbonneau, Patrick
- Physical Review E, Vol. 88, Issue 1
Scalable Metropolis Monte Carlo for simulation of hard shapes
journal, July 2016
- Anderson, Joshua A.; Eric Irrgang, M.; Glotzer, Sharon C.
- Computer Physics Communications, Vol. 204
DNA-mediated engineering of multicomponent enzyme crystals
journal, March 2015
- Brodin, Jeffrey D.; Auyeung, Evelyn; Mirkin, Chad A.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 15
Shape allophiles improve entropic assembly
journal, January 2015
- Harper, Eric S.; Marson, Ryan L.; Anderson, Joshua A.
- Soft Matter, Vol. 11, Issue 37
Entropically Patchy Particles: Engineering Valence through Shape Entropy
journal, December 2013
- van Anders, Greg; Ahmed, N. Khalid; Smith, Ross
- ACS Nano, Vol. 8, Issue 1
Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA.
journal, November 1993
- Arents, G.; Moudrianakis, E. N.
- Proceedings of the National Academy of Sciences, Vol. 90, Issue 22
General purpose molecular dynamics simulations fully implemented on graphics processing units
journal, May 2008
- Anderson, Joshua A.; Lorenz, Chris D.; Travesset, A.
- Journal of Computational Physics, Vol. 227, Issue 10
Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry
journal, September 2017
- Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael
- Science Advances, Vol. 3, Issue 9
Simplified geometric representations of protein structures identify complementary interaction interfaces
journal, November 2020
- McCafferty, Caitlyn L.; Marcotte, Edward M.; Taylor, David W.
- Proteins: Structure, Function, and Bioinformatics, Vol. 89, Issue 3
Depletion effects on the lock and key steric interactions between macromolecules
journal, January 2002
- Kinoshita, Masahiro; Oguni, Teppei
- Chemical Physics Letters, Vol. 351, Issue 1-2
Binding kinetics of lock and key colloids
journal, May 2015
- Colón-Meléndez, Laura; Beltran-Villegas, Daniel J.; van Anders, Greg
- The Journal of Chemical Physics, Vol. 142, Issue 17
Simple data and workflow management with the signac framework
journal, April 2018
- Adorf, Carl S.; Dodd, Paul M.; Ramasubramani, Vyas
- Computational Materials Science, Vol. 146
Nongenetic Approach for Imaging Protein Dimerization by Aptamer Recognition and Proximity-Induced DNA Assembly
journal, February 2018
- Liang, Hong; Chen, Shan; Li, Peipei
- Journal of the American Chemical Society, Vol. 140, Issue 12
Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces
journal, June 2015
- Gonen, S.; DiMaio, F.; Gonen, T.
- Science, Vol. 348, Issue 6241
DNA-Encoded Protein Janus Nanoparticles
journal, June 2018
- Hayes, Oliver G.; McMillan, Janet R.; Lee, Byeongdu
- Journal of the American Chemical Society, Vol. 140, Issue 29
The Role of Shape Complementarity in the Protein-Protein Interactions
journal, November 2013
- Li, Ye; Zhang, Xianren; Cao, Dapeng
- Scientific Reports, Vol. 3, Issue 1
Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study
journal, January 2014
- Fusco, Diana; Headd, Jeffrey J.; De Simone, Alfonso
- Soft Matter, Vol. 10, Issue 2
Association of Sos Ras exchange protein with Grb2 is implicated in tyrosine kinase signal transduction and transformation
journal, May 1993
- Egan, Sean E.; Giddings, Barton W.; Brooks, Mary W.
- Nature, Vol. 363, Issue 6424
Soft matter perspective on protein crystal assembly
journal, January 2016
- Fusco, Diana; Charbonneau, Patrick
- Colloids and Surfaces B: Biointerfaces, Vol. 137
Examination of shape complementarity in docking ofUnbound proteins
journal, August 1999
- Norel, Raquel; Petrey, Donald; Wolfson, Haim J.
- Proteins: Structure, Function, and Genetics, Vol. 36, Issue 3
Supercharging enables organized assembly of synthetic biomolecules
journal, January 2019
- Simon, Anna J.; Zhou, Yi; Ramasubramani, Vyas
- Nature Chemistry, Vol. 11, Issue 3
Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components
journal, March 2015
- Gerling, T.; Wagenbauer, K. F.; Neuner, A. M.
- Science, Vol. 347, Issue 6229
Dimer formation drives the activation of the cell death protease caspase 9
journal, December 2001
- Renatus, M.; Stennicke, H. R.; Scott, F. L.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 25
Understanding shape entropy through local dense packing
journal, October 2014
- van Anders, Greg; Klotsa, Daphne; Ahmed, N. Khalid
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 45
Effect of many-body interactions on the bulk and interfacial phase behavior of a model colloid-polymer mixture
journal, April 2006
- Dijkstra, Marjolein; van Roij, René; Roth, Roland
- Physical Review E, Vol. 73, Issue 4
Supramolecular Control of Enzyme Activity through Cucurbit[8]uril-Mediated Dimerization
journal, January 2013
- Dang, Dung T.; Nguyen, Hoang D.; Merkx, Maarten
- Angewandte Chemie, Vol. 125, Issue 10
HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations
journal, February 2020
- Anderson, Joshua A.; Glaser, Jens; Glotzer, Sharon C.
- Computational Materials Science, Vol. 173
Design of a hyperstable 60-subunit protein icosahedron
journal, June 2016
- Hsia, Yang; Bale, Jacob B.; Gonen, Shane
- Nature, Vol. 535, Issue 7610
A parallel algorithm for implicit depletant simulations
journal, November 2015
- Glaser, Jens; Karas, Andrew S.; Glotzer, Sharon C.
- The Journal of Chemical Physics, Vol. 143, Issue 18
Atomic-level characterization of protein–protein association
journal, February 2019
- Pan, Albert C.; Jacobson, Daniel; Yatsenko, Konstantin
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 10
Programmable molecular recognition based on the geometry of DNA nanostructures
journal, July 2011
- Woo, Sungwook; Rothemund, Paul W. K.
- Nature Chemistry, Vol. 3, Issue 8
Dimerization as a Regulatory Mechanism in Signal Transduction
journal, April 1998
- Klemm, Juli D.; Schreiber, Stuart L.; Crabtree, Gerald R.
- Annual Review of Immunology, Vol. 16, Issue 1
New Model for the Study of Liquid–Vapor Phase Transitions
journal, February 1970
- Widom, B.; Rowlinson, J. S.
- The Journal of Chemical Physics, Vol. 52, Issue 4
The role of non-specific interactions in a patchy model of protein crystallization
journal, November 2015
- Staneva, Iskra; Frenkel, Daan
- The Journal of Chemical Physics, Vol. 143, Issue 19
Modulating Nanoparticle Superlattice Structure Using Proteins with Tunable Bond Distributions
journal, January 2017
- McMillan, Janet R.; Brodin, Jeffrey D.; Millan, Jaime A.
- Journal of the American Chemical Society, Vol. 139, Issue 5
Depletion interaction of two spheres —Full density functional theory vs. morphometric results
journal, February 2009
- Oettel, M.; Hansen-Goos, H.; Bryk, P.
- EPL (Europhysics Letters), Vol. 85, Issue 3
The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients
journal, June 2020
- Premkumar, Lakshmanane; Segovia-Chumbez, Bruno; Jadi, Ramesh
- Science Immunology, Vol. 5, Issue 48