Abstract
Metalloproteins are challenging objects if we want to investigate their chemical reactivity with theoretical approaches such as density functional theory (DFT). The complexity of these biomolecules often requires us to find a compromise between accuracy and feasibility, one that is tailored to the questions we set out to answer. In this chapter, we discuss computational approaches to studying chemical reactions in metalloproteins and how to utilize the information hidden in homologous proteins.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
van Duin ACT, Dasgupta S, Lorant F et al (2001) ReaxFF: a reactive force field for hydrocarbons. J Phys Chem A 105:9396–9409
Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev 136:B864–B871
Sham LJ, Kohn W (1964) Self-consistent equations including exchange and correlation effects. Phys Rev 140:A1133–A1138
Harvey JN (2004) DFT computation of relative spin-state energetics of transition metal compounds. Struct Bond 112:151–183
Siegbahn PEM, Himo F (2011) The quantum chemical cluster approach for modeling enzyme reactions. Wiley Interdiscip Rev Comput Mol Sci 1:323–336
O’Boyle NM, Banck M, James CA et al (2011) Open Babel: an open chemical toolbox. J Cheminform 3:33
Sondergaard CR, Olsson MHM, Rostkowski M et al (2011) Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. J Chem Theory Comput 7:2284–2295
Olsson MHM, Sondergaard CR, Rostowski M et al (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput 7:525–537
Klamt A, Schüürmann G (1993) COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans 2:799–805
Jacob CR, Neugebauer J (2014) Subsystem density-functional theory. WIREs Comput Mol Sci 4:325–362
Slater JC (1951) A simplification of the Hartree-Fock method. Phys Rev 81:385–390
Vosko SH, Wilk L, Nusair M (1980) Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can J Phys 81:1200–1211
Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865–3868
Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098–3100
Tao J, Perdew JP, Staroverov VN et al (2003) Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids. Phys Rev Lett 91:146401
Zhao Y, Truhlar DG (2006) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent nteractions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor Chem Accounts 120:215–241
Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652
Perdew JP, Zupan S, Blaha P (1999) Accurate density functional with correct formal properties: a step beyond the generalized gradient approximation. Phys Rev Lett 82:2544–2547
Perdew JP, Tao J, Staroverov VN et al (2004) Meta-generalized gradient approximation: explanation of a realistic nonempirical density functional. J Chem Phys 120:6898–6911
Perdew JP, Ernzerhof M, Burke K (1996) Rationale for mixing exact exchange with density functional approximations. J Chem Phys 105:9982–9985
Grimme S (2004) Accurate description of van der Waals complexes by density functional theory including empirical corrections. J Comput Chem 25:1463–1473
Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion contribution. J Comput Chem 27:1787–1799
Grimme S, Antony J, Ehrlich S et al (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132:154104
Valiev M, Bylaska EJ, Govind N et al (2010) NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations. Comput Phys Commun 181:1477
te Velde F, Bickelhaupt FM, Baerends EJ et al (2001) Chemistry with ADF. J Comput Chem 22:931–967
Hoffmann R (1963) An extended Hückel theory. I. Hydrocarbons. J Chem Phys 39:1397–1412
Frisch MJ, Trucks GW, Schlegel HB et al (2009) Gaussian 09, Revision E.01. Gaussian, Wallingford CT
Klamt A (1995) Conductor-like screening model for real solvents: a new approach to the quantitative calculation of solvation phenomena. J Phys Chem 99:2224–2235
Mills F, Jónsson H, Schenter GK (1995) Reversible work transition state theory: application to dissociative adsorption of hydrogen. Surf Sci 324:305–337
Peng C, Schlegel JB (1993) Combining synchronous transit and quasi-Newton methods for finding transition states. Israel J Chem 33:449–454
Neese F (2012) The ORCA program system. Wiley Interdiscip Rev Comput Mol Sci 2:73–78
Stiebritz MT, Hiller CJ, Sickerman NS et al (2018) Ambient conversion of CO2 to hydrocarbons by biogenic and synthetic [Fe4S4] clusters. Nat Catal in press
Noodleman J (1981) Valence bond description of antiferromagnetic coupling in transition metal dimers. J Chem Phys 74:5737–5743
Noodleman J, Post D, Baerends E (1982) Symmetry breaking and ionization from symmetry equivalent inner shells, and lone pairs in Xα theory. Chem Phys 64:159–166
Noodleman J, Peng CY, Case DA et al (1995) Orbital interactions, electron delocalization and spin coupling in iron-sulfur clusters. Coord Chem 144:199–244
Lovell T, Li J, Liu T et al (2001) FeMo cofactor of nitrogenase: a density functional study of states MN, MOX, MR, and MI. J Am Chem Soc 123:12392–12410
Rebelein JG, Stiebritz MT, Lee CC et al (2017) Activation and reduction of carbon dioxide by nitrogenase iron proteins. Nat Chem Biol 13:147–149
Strop P, Takahara PM, Chiu H et al (2001) Crystal structure of the all-ferrous [4Fe-4S]0 form of the nitrogenase iron protein from Azotobacter vinelandii. Biochemistry 40:651–656
Schäfer A, Huber C, Ahlrichs R (1994) Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr. J Chem Phys 100:5829–5836
Weigend F, Ahlrichs R (2005) Balanced basis sets of split alence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy. Phys Chem Chem Phys 7:3297–3305
Schäfer A, Horn H, Ahrichs R (1992) Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J Chem Phys 97:2571–2577
Eichkorn K, Weigend F, Treutler O et al (1997) Auxiliary basis sets for main row atoms and transition metals and their use to approximate coulomb potentials. Theor Chem Accounts 97:119–124
Weigend F (2006) Accurate coulomb-fitting basis sets for H to Rn. Phys Chem Chem Phys 8:1057–1065
Martί-Renom MA, Stuart AC, Fiser A et al (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325
Lesk AM, Chothia C (1980) How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol 136:225–270
Arnold K, Bordoli L, Kopp J et al (2006) The SWISS-MODEL workspace: a web based environment for protein structure homology modelling. Bioinformatics 22:195–201
Guex N, Peitsch MC, Schwede T (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis 30:S162–S173
Kiefer F, Arnold K, Künzli M et al (2009) The Swiss-model repository and associated resources. Nucleic Acids Res 37:D387–D392
Biasini M, Bienert S, Waterhouse A et al (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258
Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815
Webb B, Sali A (2014) Comparative protein structure modeling using modeller. Curr Protoc Bioinformatics 47:5.6.1–5.6.32
Benkert P, Tosatto SC, Schomburg D (2008) QMEAN: a comprehensive scoring function for model quality assessment. Proteins 71:261–277
Li L, Li C, Sarkar S et al (2012) DelPhi: a comprehensive suite for DelPhi software and associated resources. BMC Biophys 5:9
Baker NA, Sept D, Joseph S et al (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98:10037–10041
Finkelmann AR, Stiebritz MT, Reiher M (2013) Electric-field effects on the [FeFe]-hydrogenase active site. Chem Commun 49:8099–8101
Dolinsky TJ, Nielsen JE, McCammon JA et al (2004) PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32:W665–W667
Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98:1978–1988
Warshel A, Levitt M (1976) Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103:227–249
Field MJ, Bash PA, Karplus M (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J Comput Chem 11:700–733
Gao J (1996) Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent ffects in organic chemistry. Acc Chem Res 29:298–305
Svensson M, Humbel S, Froese RDJ et al (1996) ONIOM: a multilayered integrated MO + MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)3)2 + H2 oxidative addition. J Phys Chem 100:19357–19363
Metz S, Kästner J, Sokol AA et al (2014) ChemShell – a molecular software package for QM/MM simulations. WIREs Comput Mol Sci 4:101–110
Ryde U (1996) The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum chemical and molecular mechanical calculations. J Comput Aided Mol Des 10:153–164
Ryde U, Olsson MH (2001) Structure, strain, and reorganization energy of blue copper models in the protein. Int J Quant Chem 81:335–347
Lin H, Truhlar DG (2007) QM/MM: what have we learned, where are we, and where do we go from here? Theor Chem Accounts 117:185–199
Senn HM, Thiel W (2007) QM/MM studies of enzymes. Curr Opin Chem Biol 11:182–187
Ryde U (2003) Combined quantum and molecular mechanics calculations on metalloproteins. Curr Opin Chem Biol 7:136–142
Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed Engl 48:1198–1229
Case DA, Cerutti DS, Cheatham TE III et al (2017) Amber. University of California, San Francisco
Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the Amber biomolecular simulation package. WIREs Comput Mol Sci 3:198–210
Bayly CI, Cieplak P, Cornell WD et al (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP method. J Phys Chem 97:10269–10280
Hoops SC, Anderson KW, Merz KM (1991) Force field design for metalloproteins. J Am Chem Soc 113:8262–8270
Ryde U (1995) Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. Proteins 21:40–56
Seminario JM (1996) Calculation of intramolecular force fields from second-derivative tensors. Int J Quantum Chem 60:1271–1277
Burger SK, Lacasse M, Verstraelen T et al (2012) Automated parametrization of AMBER force field terms from vibrational analysis with a focus on functionalizing dinuclear zinc(II) scaffolds. J Chem Theory Comput 8:554–562
Nilsson K, Lecerof D, Sigfridsson E et al (2003) An automatic method to generate force-field parameters for hetero-compounds. Acta Crystallogr Sect D 59:274–289
Vanduyfhuys L, Vandenbrande S, Verstraelen T et al (2015) QuickFF: a program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input. J Comp Chem 36:1015–1027
Zheng S, Tang Q, He J et al (2016) VFFDT: a new software for preparing AMBER force field parameters for metal-containing molecular systems. J Chem Inf Model 56:811–818
Li P, Merz KM (2016) MCBP.py: a python based metal center parameter builder. J Chem Inf Model 56:599–604
Stiebritz MT (2015) MetREx: a protein design approach for the exploration of sequence-reactivity relationships in metalloenzymes. J Comput Chem 36:553–563
Stiebritz MT, Wengrzik S, Klein DL et al (2010) Computational design of a chain-specific tetracycline repressor heterodimer. J Mol Biol 403:371–385
Stiebritz MT, Muller YA (2006) MUMBO: a protein-design approach to crystallographic model building and refinement. Acta Crystallogr Sect D 62:648–658
Acknowledgments
The authors are supported by the National Science Foundation CAREER award CHE-1651398 (to Y.H.).
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Stiebritz, M.T., Hu, Y. (2019). Computational Methods for Modeling Metalloproteins. In: Hu, Y. (eds) Metalloproteins. Methods in Molecular Biology, vol 1876. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8864-8_16
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8864-8_16
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8863-1
Online ISBN: 978-1-4939-8864-8
eBook Packages: Springer Protocols