Chimeric Cellobiose Dehydrogenases Reveal the Function of Cytochrome Domain Mobility for the Electron Transfer to Lytic Polysaccharide Monooxygenase

. 2021 Jan 15 ; 11 (2) : 517-532. [epub] 20201224

Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid33489432

Grantová podpora
W 1224 Austrian Science Fund FWF - Austria

The natural function of cellobiose dehydrogenase (CDH) to donate electrons from its catalytic flavodehydrogenase (DH) domain via its cytochrome (CYT) domain to lytic polysaccharide monooxygenase (LPMO) is an example of a highly efficient extracellular electron transfer chain. To investigate the function of the CYT domain movement in the two occurring electron transfer steps, two CDHs from the ascomycete Neurospora crassa (NcCDHIIA and NcCDHIIB) and five chimeric CDH enzymes created by domain swapping were studied in combination with the fungus' own LPMOs (NcLPMO9C and NcLPMO9F). Kinetic and electrochemical methods and hydrogen/deuterium exchange mass spectrometry were used to study the domain movement, interaction, and electron transfer kinetics. Molecular docking provided insights into the protein-protein interface, the orientation of domains, and binding energies. We find that the first, interdomain electron transfer step from the catalytic site in the DH domain to the CYT domain depends on steric and electrostatic interface complementarity and the length of the protein linker between both domains but not on the redox potential difference between the FAD and heme b cofactors. After CYT reduction, a conformational change of CDH from its closed state to an open state allows the second, interprotein electron transfer (IPET) step from CYT to LPMO to occur by direct interaction of the b-type heme and the type-2 copper center. Chimeric CDH enzymes favor the open state and achieve higher IPET rates by exposing the heme b cofactor to LPMO. The IPET, which is influenced by interface complementarity and the heme b redox potential, is very efficient with bimolecular rates between 2.9 × 105 and 1.1 × 106 M-1 s-1.

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Langston J. A.; Shaghasi T.; Abbate E.; Xu F.; Vlasenko E.; Sweeney M. D. Oxidoreductive Cellulose Depolymerization by the Enzymes Cellobiose Dehydrogenase and Glycoside Hydrolase 61. Appl. Environ. Microbiol. 2011, 77, 7007–7015. 10.1128/aem.05815-11. PubMed DOI PMC

Phillips C. M.; Beeson W. T.; Cate J. H.; Marletta M. A. Cellobiose Dehydrogenase and a Copper-Dependent Polysaccharide Monooxygenase Potentiate Cellulose Degradation by Neurospora crassa. ACS Chem. Biol. 2011, 6, 1399–1406. 10.1021/cb200351y. PubMed DOI

Phillips C. M.; Iavarone A. T.; Marletta M. A. Quantitative Proteomic Approach for Cellulose Degradation by Neurospora crassa. J. Proteome Res. 2011, 10, 4177–4185. 10.1021/pr200329b. PubMed DOI

Harris P. V.; Welner D.; McFarland K. C.; Re E.; Navarro Poulsen J.-C.; Brown K.; Salbo R.; Ding H.; Vlasenko E.; Merino S.; Xu F.; Cherry J.; Larsen S.; Lo Leggio L. Stimulation of Lignocellulosic Biomass Hydrolysis by Proteins of Glycoside Hydrolase Family 61: Structure and Function of a Large, Enigmatic Family. Biochemistry 2010, 49, 3305–3316. 10.1021/bi100009p. PubMed DOI

Quinlan R. J.; Sweeney M. D.; Lo Leggio L.; Otten H.; Poulsen J.-C. N.; Johansen K. S.; Krogh K. B. R. M.; Jorgensen C. I.; Tovborg M.; Anthonsen A.; Tryfona T.; Walter C. P.; Dupree P.; Xu F.; Davies G. J.; Walton P. H. Insights into the Oxidative Degradation of Cellulose by a Copper Metalloenzyme That Exploits Biomass Components. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 15079–15084. 10.1073/pnas.1105776108. PubMed DOI PMC

Kracher D.; Scheiblbrandner S.; Felice A. K. G.; Breslmayr E.; Preims M.; Ludwicka K.; Haltrich D.; Eijsink V. G. H.; Ludwig R. Extracellular Electron Transfer Systems Fuel Cellulose Oxidative Degradation. Science 2016, 352, 1098–1101. 10.1126/science.aaf3165. PubMed DOI

Sygmund C.; Kracher D.; Scheiblbrandner S.; Zahma K.; Felice A. K. G.; Harreither W.; Kittl R.; Ludwig R. Characterization of the Two Neurospora crassa Cellobiose Dehydrogenases and Their Connection to Oxidative Cellulose Degradation. Appl. Environ. Microbiol. 2012, 78, 6161–6171. 10.1128/aem.01503-12. PubMed DOI PMC

Igarashi K.; Yoshida M.; Matsumura H.; Nakamura N.; Ohno H.; Samejima M.; Nishino T. Electron Transfer Chain Reaction of the Extracellular Flavocytochrome Cellobiose Dehydrogenase from the Basidiomycete Phanerochaete chrysosporium. FEBS J. 2005, 272, 2869–2877. 10.1111/j.1742-4658.2005.04707.x. PubMed DOI

Tan T.-C.; Kracher D.; Gandini R.; Sygmund C.; Kittl R.; Haltrich D.; Hällberg B. M.; Ludwig R.; Divne C. Structural Basis for Cellobiose Dehydrogenase Action during Oxidative Cellulose Degradation. Nat. Commun. 2015, 6, 7542.10.1038/ncomms8542. PubMed DOI PMC

Igarashi K.; Momohara I.; Nishino T.; Samejima M. Kinetics of Inter-Domain Electron Transfer in Flavocytochrome Cellobiose Dehydrogenase from the White-Rot Fungus Phanerochaete chrysosporium. Biochem. J. 2002, 365, 521.10.1042/bj20011809. PubMed DOI PMC

Kracher D.; Zahma K.; Schulz C.; Sygmund C.; Gorton L.; Ludwig R. Inter-Domain Electron Transfer in Cellobiose Dehydrogenase: Modulation by pH and Divalent Cations. FEBS J. 2015, 282, 3136–3148. 10.1111/febs.13310. PubMed DOI PMC

Bodenheimer A. M.; O’Dell W. B.; Oliver R. C.; Qian S.; Stanley C. B.; Meilleur F. Structural Investigation of Cellobiose Dehydrogenase IIA: Insights from Small Angle Scattering into Intra- and Intermolecular Electron Transfer Mechanisms. Biochim. Biophys. Acta, Gen. Subj. 2018, 1862, 1031–1039. 10.1016/j.bbagen.2018.01.016. PubMed DOI

Bodenheimer A. M.; O’Dell W. B.; Stanley C. B.; Meilleur F. Structural Studies of Neurospora crassa LPMO9D and Redox Partner CDHIIA Using Neutron Crystallography and Small-Angle Scattering. Carbohydr. Res. 2017, 448, 200–204. 10.1016/j.carres.2017.03.001. PubMed DOI

Harada H.; Onoda A.; Uchihashi T.; Watanabe H.; Sunagawa N.; Samejima M.; Igarashi K.; Hayashi T. Interdomain Flip-Flop Motion Visualized in Flavocytochrome Cellobiose Dehydrogenase Using High-Speed Atomic Force Microscopy during Catalysis. Chem. Sci. 2017, 8, 6561–6565. 10.1039/c7sc01672g. PubMed DOI PMC

Courtade G.; Wimmer R.; Røhr Å. K.; Preims M.; Felice A. K. G.; Dimarogona M.; Vaaje-Kolstad G.; Sørlie M.; Sandgren M.; Ludwig R.; Eijsink V. G. H.; Aachmann F. L. Interactions of a Fungal Lytic Polysaccharide Monooxygenase with β-Glucan Substrates and Cellobiose Dehydrogenase. Proc. Natl. Acad. Sci. U.S.A. 2016, 113, 5922–5927. 10.1073/pnas.1602566113. PubMed DOI PMC

Laurent C. V. F. P.; Breslmayr E.; Tunega D.; Ludwig R.; Oostenbrink C. Interaction between Cellobiose Dehydrogenase and Lytic Polysaccharide Monooxygenase. Biochemistry 2019, 58, 1226–1235. 10.1021/acs.biochem.8b01178. PubMed DOI PMC

Ortiz R.; Matsumura H.; Tasca F.; Zahma K.; Samejima M.; Igarashi K.; Ludwig R.; Gorton L. Effect of Deglycosylation of Cellobiose Dehydrogenases on the Enhancement of Direct Electron Transfer with Electrodes. Anal. Chem. 2012, 84, 10315–10323. 10.1021/ac3022899. PubMed DOI

Hallberg B. M.; Henriksson G.; Pettersson G.; Divne C. Crystal Structure of the Flavoprotein Domain of the Extracellular Flavocytochrome Cellobiose Dehydrogenase. J. Mol. Biol. 2002, 315, 421–434. 10.1006/jmbi.2001.5246. PubMed DOI

Zamocky M.; Ludwig R.; Peterbauer C.; Hallberg B.; Divne C.; Nicholls P.; Haltrich D. Cellobiose Dehydrogenase-a Flavocytochrome from Wood-Degrading, Phytopathogenic and Saprotropic Fungi. Curr. Protein Pept. Sci. 2006, 7, 255–280. 10.2174/138920306777452367. PubMed DOI

Mason M. G.; Wilson M. T.; Ball A.; Nicholls P. Oxygen Reduction by Cellobiose Oxidoreductase: The Role of the Haem Group. FEBS Lett. 2002, 518, 29–32. 10.1016/s0014-5793(02)02633-9. PubMed DOI

Mason M. G.; Nicholls P.; Divne C.; Hallberg B. M.; Henriksson G.; Wilson M. T. The Heme Domain of Cellobiose Oxidoreductase: A One-Electron Reducing System. Biochim. Biophys. Acta, Rev. Bioenerg. 2003, 1604, 47–54. 10.1016/s0005-2728(03)00023-9. PubMed DOI

Samejima M.; Phillips R. S.; Eriksson K.-E. L. Cellobiose Oxidase from Phanerochaete chrysosporium Stopped-Flow Spectrophotometric Analysis of pH-Dependent Reduction. FEBS Lett. 1992, 306, 165–168. 10.1016/0014-5793(92)80991-o. PubMed DOI

Moser C. C.; Keske J. M.; Warncke K.; Farid R. S.; Dutton P. L. Nature of Biological Electron Transfer. Nature 1992, 355, 796–802. 10.1038/355796a0. PubMed DOI

Page C. C.; Moser C. C.; Chen X.; Dutton P. L. Natural Engineering Principles of Electron Tunnelling in Biological Oxidation–Reduction. Nature 1999, 402, 47–52. 10.1038/46972. PubMed DOI

Dominguez C.; Boelens R.; Bonvin A. M. J. J. HADDOCK: A Protein–Protein Docking Approach Based on Biochemical or Biophysical Information. J. Am. Chem. Soc. 2003, 125, 1731–1737. 10.1021/ja026939x. PubMed DOI

de Vries S. J.; van Dijk A. D. J.; Krzeminski M.; van Dijk M.; Thureau A.; Hsu V.; Wassenaar T.; Bonvin A. M. J. J. HADDOCK versus HADDOCK: New Features and Performance of HADDOCK2.0 on the CAPRI Targets. Proteins: Struct., Funct., Bioinf. 2007, 69, 726–733. 10.1002/prot.21723. PubMed DOI

Eichenberger A. P.; Allison J. R.; Dolenc J.; Geerke D. P.; Horta B. A. C.; Meier K.; Oostenbrink C.; Schmid N.; Steiner D.; Wang D.; van Gunsteren W. F. GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories. J. Chem. Theory Comput. 2011, 7, 3379–3390. 10.1021/ct2003622. PubMed DOI

de Ruiter A.; Oostenbrink C. Protein–Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations. J. Chem. Theory Comput. 2013, 9, 883–892. 10.1021/ct300967a. PubMed DOI

Xue L. C.; Rodrigues J. P.; Kastritis P. L.; Bonvin A. M.; Vangone A. PRODIGY: A Web Server for Predicting the Binding Affinity of Protein-Protein Complexes. Bioinformatics 2016, 32, 3676–3678. 10.1093/bioinformatics/btw514. PubMed DOI

Kastritis P. L.; Rodrigues J. P. G. L. M.; Folkers G. E.; Boelens R.; Bonvin A. M. J. J. Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface. J. Mol. Biol. 2014, 426, 2632–2652. 10.1016/j.jmb.2014.04.017. PubMed DOI

Vangone A.; Bonvin A. M. Contacts-Based Prediction of Binding Affinity in Protein-Protein Complexes. eLife 2015, 4, e0745410.7554/elife.07454. PubMed DOI PMC

Janin J.; Bahadur R. P.; Chakrabarti P. Protein–Protein Interaction and Quaternary Structure. Q. Rev. Biophys. 2008, 41, 133–180. 10.1017/s0033583508004708. PubMed DOI

Li X.; Beeson W. T.; Phillips C. M.; Marletta M. A.; Cate J. H. D. Structural Basis for Substrate Targeting and Catalysis by Fungal Polysaccharide Monooxygenases. Structure 2012, 20, 1051–1061. 10.1016/j.str.2012.04.002. PubMed DOI PMC

Kittl R.; Kracher D.; Burgstaller D.; Haltrich D.; Ludwig R. Production of Four Neurospora crassa Lytic Polysaccharide Monooxygenases in Pichia Pastoris Monitored by a Fluorimetric Assay. Biotechnol. Biofuels 2012, 5, 79.10.1186/1754-6834-5-79. PubMed DOI PMC

Kadek A.; Kavan D.; Felice A. K. G.; Ludwig R.; Halada P.; Man P. Structural Insight into the Calcium Ion Modulated Interdomain Electron Transfer in Cellobiose Dehydrogenase. FEBS Lett. 2015, 589, 1194–1199. 10.1016/j.febslet.2015.03.029. PubMed DOI

Konermann L.; Vahidi S.; Sowole M. A. Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules. Anal. Chem. 2014, 86, 213–232. 10.1021/ac4039306. PubMed DOI

Sowole M. A.; Konermann L. Effects of Protein–Ligand Interactions on Hydrogen/Deuterium Exchange Kinetics: Canonical and Noncanonical Scenarios. Anal. Chem. 2014, 86, 6715–6722. 10.1021/ac501849n. PubMed DOI

Lindgren A.; Larsson T.; Ruzgas T.; Gorton L. Direct Electron Transfer between the Heme of Cellobiose Dehydrogenase and Thiol Modified Gold Electrodes. J. Electroanal. Chem. 2000, 494, 105–113. 10.1016/s0022-0728(00)00326-0. DOI

Nicholson R. S. Theory and Application of Cyclic Voltammetry for Measurement of Electrode Reaction Kinetics. Anal. Chem. 1965, 37, 1351–1355. 10.1021/ac60230a016. DOI

Bowden E. F.; Hawkridge F. M.; Blount H. N. Interfacial Electrochemistry of Cytochrome c at Tin Oxide, Indium Oxide, Gold, and Platinum Electrodes. J. Electroanal. Chem. Interfacial Electrochem. 1984, 161, 355–376. 10.1016/s0022-0728(84)80193-x. DOI

Raices M.; Paifer E.; Cremata J.; Montesino R.; Ståhlberg J.; Divne C.; Szabó I. J.; Henriksson G.; Johansson G.; Pettersson G. Cloning and Characterization of a CDNA Encoding a Cellobiose Dehydrogenase from the White Rot Fungus Phanerochaete chrysosporium. FEBS Lett. 1995, 369, 233–238. 10.1016/0014-5793(95)00758-2. PubMed DOI

Hallberg B. M.; Bergfors T.; Bäckbro K.; Pettersson G.; Henriksson G.; Divne C. A New Scaffold for Binding Haem in the Cytochrome Domain of the Extracellular Flavocytochrome Cellobiose Dehydrogenase. Structure 2000, 8, 79–88. 10.1016/s0969-2126(00)00082-4. PubMed DOI

Diêp Lê K. H.; Lederer F.; Golinelli-Pimpaneau B. Structural Evidence for the Functional Importance of the Heme Domain Mobility in Flavocytochrome b2. J. Mol. Biol. 2010, 400, 518–530. 10.1016/j.jmb.2010.05.035. PubMed DOI

Vaaje-Kolstad G.; Westereng B.; Horn S. J.; Liu Z.; Zhai H.; Sørlie M.; Eijsink V. G. H. An Oxidative Enzyme Boosting the Enzymatic Conversion of Recalcitrant Polysaccharides. Science 2010, 330, 219–222. 10.1126/science.1192231. PubMed DOI

Kadek A.; Kavan D.; Marcoux J.; Stojko J.; Felice A. K. G.; Cianférani S.; Ludwig R.; Halada P.; Man P. Interdomain Electron Transfer in Cellobiose Dehydrogenase Is Governed by Surface Electrostatics. Biochim. Biophys. Acta, Gen. Subj. 2017, 1861, 157–167. 10.1016/j.bbagen.2016.11.016. PubMed DOI

Harreither W.; Sygmund C.; Augustin M.; Narciso M.; Rabinovich M. L.; Gorton L.; Haltrich D.; Ludwig R. Catalytic Properties and Classification of Cellobiose Dehydrogenases from Ascomycetes. Appl. Environ. Microbiol. 2011, 77, 1804–1815. 10.1128/aem.02052-10. PubMed DOI PMC

Jones S. M.; Transue W. J.; Meier K. K.; Kelemen B.; Solomon E. I. Kinetic Analysis of Amino Acid Radicals Formed in H2O2-Driven CuI LPMO Reoxidation Implicates Dominant Homolytic Reactivity. Proc. Natl. Acad. Sci. U.S.A. 2020, 117, 11916–11922. 10.1073/pnas.1922499117. PubMed DOI PMC

Paradisi A.; Johnston E. M.; Tovborg M.; Nicoll C. R.; Ciano L.; Dowle A.; McMaster J.; Hancock Y.; Davies G. J.; Walton P. H. Formation of a Copper(II)–Tyrosyl Complex at the Active Site of Lytic Polysaccharide Monooxygenases Following Oxidation by H2O2. J. Am. Chem. Soc. 2019, 141, 18585–18599. 10.1021/jacs.9b09833. PubMed DOI PMC

Chylenski P.; Bissaro B.; Sørlie M.; Røhr Å. K.; Várnai A.; Horn S. J.; Eijsink V. G. H. Lytic Polysaccharide Monooxygenases in Enzymatic Processing of Lignocellulosic Biomass. ACS Catal. 2019, 9, 4970–4991. 10.1021/acscatal.9b00246. DOI

Petrović D. M.; Várnai A.; Dimarogona M.; Mathiesen G.; Sandgren M.; Westereng B.; Eijsink V. G. H. Comparison of Three Seemingly Similar Lytic Polysaccharide Monooxygenases from Neurospora crassa Suggests Different Roles in Plant Biomass Degradation. J. Biol. Chem. 2019, 294, 15068–15081. 10.1074/jbc.RA119.008196. PubMed DOI PMC

Loose J. S. M.; Forsberg Z.; Kracher D.; Scheiblbrandner S.; Ludwig R.; Eijsink V. G. H.; Vaaje-Kolstad G. Activation of Bacterial Lytic Polysaccharide Monooxygenases with Cellobiose Dehydrogenase. Protein Sci. 2016, 25, 2175–2186. 10.1002/pro.3043. PubMed DOI PMC

Tamura K.; Stecher G.; Peterson D.; Filipski A.; Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 2013, 30, 2725–2729. 10.1093/molbev/mst197. PubMed DOI PMC

Harreither W.; Felice A. K. G.; Paukner R.; Gorton L.; Ludwig R.; Sygmund C. Recombinantly Produced Cellobiose Dehydrogenase from Corynascus thermophilus for Glucose Biosensors and Biofuel Cells. Biotechnol. J. 2012, 7, 1359–1366. 10.1002/biot.201200049. PubMed DOI

Weis R.; Luiten R.; Skranc W.; Schwab H.; Wubbolts M.; Glieder A. Reliable High-Throughput Screening with Pichia Pastoris by Limiting Yeast Cell Death Phenomena. FEMS Yeast Res. 2004, 5, 179–189. 10.1016/j.femsyr.2004.06.016. PubMed DOI

McIlvaine T. C. A Buffer Solution for Colorimetric Comparison. J. Biol. Chem. 1921, 49, 183–186.

Gasteiger E.; Hoogland C.; Gattiker A.; Duvaud S.; Wilkins M. R.; Appel R. D.; Bairoch A.. Protein Identification and Analysis Tools on the ExPASy Server. In The Proteomics Protocols Handbook; Walker J. M., Ed.; Humana Press: Totowa, NJ, 2005; pp 571–607.

Nicholson R. S.; Shain I. Theory of Stationary Electrode Polarography. Single Scan and Cyclic Methods Applied to Reversible, Irreversible, and Kinetic Systems. Anal. Chem. 1964, 36, 706–723. 10.1021/ac60210a007. DOI

Matsuda H. Zur Theorie der Wechselspannungs-Polarographie. Z. für Elektrochem. Berichte Bunsenges. für Phys. Chem. 1958, 62, 977–989. 10.1002/bbpc.19580620909. DOI

Ševčík A. Oscillographic Polarography with Periodical Triangular Voltage. Collect. Czech. Chem. Commun. 1948, 13, 349–377. 10.1135/cccc19480349. DOI

Randles J. E. B. A Cathode Ray Polarograph Part II.—The Current-Voltage Curves. Trans. Faraday Soc. 1948, 44, 327–338. 10.1039/tf9484400327. DOI

Arnold K.; Bordoli L.; Kopp J.; Schwede T. The SWISS-MODEL Workspace: A Web-Based Environment for Protein Structure Homology Modelling. Bioinformatics 2006, 22, 195–201. 10.1093/bioinformatics/bti770. PubMed DOI

Benkert P.; Biasini M.; Schwede T. Toward the Estimation of the Absolute Quality of Individual Protein Structure Models. Bioinformatics 2011, 27, 343–350. 10.1093/bioinformatics/btq662. PubMed DOI PMC

Biasini M.; Bienert S.; Waterhouse A.; Arnold K.; Studer G.; Schmidt T.; Kiefer F.; Cassarino T. G.; Bertoni M.; Bordoli L.; Schwede T. SWISS-MODEL: Modelling Protein Tertiary and Quaternary Structure Using Evolutionary Information. Nucleic Acids Res. 2014, 42, W252–W258. 10.1093/nar/gku340. PubMed DOI PMC

Schmid N.; Christ C. D.; Christen M.; Eichenberger A. P.; van Gunsteren W. F. Architecture, Implementation and Parallelisation of the GROMOS Software for Biomolecular Simulation. Comput. Phys. Commun. 2012, 183, 890–903. 10.1016/j.cpc.2011.12.014. DOI

Schmid N.; Eichenberger A. P.; Choutko A.; Riniker S.; Winger M.; Mark A. E.; van Gunsteren W. F. Definition and Testing of the GROMOS Force-Field Versions 54A7 and 54B7. Eur. Biophys. J. 2011, 40, 843–856. 10.1007/s00249-011-0700-9. PubMed DOI

Poger D.; Van Gunsteren W. F.; Mark A. E. A New Force Field for Simulating Phosphatidylcholine Bilayers. J. Comput. Chem. 2010, 31, 1117–1125. 10.1002/jcc.21396. PubMed DOI

Olsson M. H. M.; Søndergaard C. R.; Rostkowski M.; Jensen J. H. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J. Chem. Theory Comput. 2011, 7, 525–537. 10.1021/ct100578z. PubMed DOI

Søndergaard C. R.; Olsson M. H. M.; Rostkowski M.; Jensen J. H. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. J. Chem. Theory Comput. 2011, 7, 2284–2295. 10.1021/ct200133y. PubMed DOI

Dolinsky T. J.; Nielsen J. E.; McCammon J. A.; Baker N. A. PDB2PQR: An Automated Pipeline for the Setup of Poisson–Boltzmann Electrostatics Calculations. Nucleic Acids Res. 2004, 32, W665–W667. 10.1093/nar/gkh381. PubMed DOI PMC

Baker N. A.; Sept D.; Joseph S.; Holst M. J.; McCammon J. A. Electrostatics of Nanosystems: Application to Microtubules and the Ribosome. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037–10041. 10.1073/pnas.181342398. PubMed DOI PMC

Bank R. E.; Holst M. A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Rev. 2003, 45, 291–323. 10.1137/s003614450342061. DOI

Holst M. Adaptive Numerical Treatment of Elliptic Systems on Manifolds. Adv. Comput. Math. 2001, 15, 139–191. 10.1023/a:1014246117321. DOI

Holst M.; Saied F. Multigrid Solution of the Poisson—Boltzmann Equation. J. Comput. Chem. 1993, 14, 105–113. 10.1002/jcc.540140114. DOI

Holst M. J.; Saied F. Numerical Solution of the Nonlinear Poisson–Boltzmann Equation: Developing More Robust and Efficient Methods. J. Comput. Chem. 1995, 16, 337–364. 10.1002/jcc.540160308. DOI

Kastritis P. L.; Rodrigues J. P. G. L. M.; Folkers G. E.; Boelens R.; Bonvin A. M. J. J. Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface. J. Mol. Biol. 2014, 426, 2632–2652. 10.1016/j.jmb.2014.04.017. PubMed DOI

Vangone A.; Bonvin A. M. Contacts-Based Prediction of Binding Affinity in Protein–Protein Complexes. eLife 2015, 4, e0745410.7554/elife.07454. PubMed DOI PMC

Xue L. C.; Rodrigues J. P.; Kastritis P. L.; Bonvin A. M.; Vangone A. PRODIGY: A Web Server for Predicting the Binding Affinity of Protein–Protein Complexes. Bioinformatics 2016, 32, 3676–3678. 10.1093/bioinformatics/btw514. PubMed DOI

Lê S.; Josse J.; Husson F. FactoMineR: An R Package for Multivariate Analysis. J. Stat. Software 2008, 25, 1.10.18637/jss.v025.i01. DOI

Revelle W. R.Psych: Procedures for Personality and Psychological Research, 2017.

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