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Carter-Fenk K, Liu M, Pujal L, Loipersberger M, Tsanai M, Vernon RM, Forman-Kay JD, Head-Gordon M, Heidar-Zadeh F, Head-Gordon T. The Energetic Origins of Pi-Pi Contacts in Proteins. J Am Chem Soc 2023; 145. [PMID: 37917924 PMCID: PMC10655088 DOI: 10.1021/jacs.3c09198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein's stability and structure. Pi-pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi-pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi-pi contact motifs. We find that neutral pi-pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter-Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi-pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi-pi contacts in polar media and like typical ion-pi interactions in nonpolar environments. Like-charged pairs such as arginine-arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi-pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.
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Affiliation(s)
- Kevin Carter-Fenk
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Meili Liu
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Leila Pujal
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Matthias Loipersberger
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Maria Tsanai
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Robert M. Vernon
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Julie D. Forman-Kay
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Martin Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Farnaz Heidar-Zadeh
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
- Center
for Molecular Modeling (CMM), Ghent University, 9052 Zwijnaarde, Belgium
| | - Teresa Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
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Pujal L, van Zyl M, Vöhringer-Martinez E, Verstraelen T, Bultinck P, Ayers PW, Heidar-Zadeh F. Constrained iterative Hirshfeld charges: A variational approach. J Chem Phys 2022; 156:194109. [PMID: 35597660 DOI: 10.1063/5.0089466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We develop a variational procedure for the iterative Hirshfeld (HI) partitioning scheme. The main practical advantage of having a variational framework is that it provides a formal and straightforward approach for imposing constraints (e.g., fixed charges on certain atoms or molecular fragments) when computing HI atoms and their properties. Unlike many other variants of the Hirshfeld partitioning scheme, HI charges do not arise naturally from the information-theoretic framework, but only as a reverse-engineered construction of the objective function. However, the procedure we use is quite general and could be applied to other problems as well. We also prove that there is always at least one solution to the HI equations, but we could not prove that its self-consistent equations would always converge for any given initial pro-atom charges. Our numerical assessment of the constrained iterative Hirshfeld method shows that it satisfies many desirable traits of atoms in molecules and has the potential to surpass existing approaches for adding constraints when computing atomic properties.
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Affiliation(s)
- Leila Pujal
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7N 3N6, Canada
| | - Maximilian van Zyl
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7N 3N6, Canada
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052 Zwijnaarde, Belgium
| | - Patrick Bultinck
- Ghent Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan 281 S3, B-9000 Ghent, Belgium
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7N 3N6, Canada
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Verstraelen T, Adams W, Pujal L, Tehrani A, Kelly BD, Macaya L, Meng F, Richer M, Hernández-Esparza R, Yang XD, Chan M, Kim TD, Cools-Ceuppens M, Chuiko V, Vöhringer-Martinez E, Ayers PW, Heidar-Zadeh F. IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files. J Comput Chem 2021; 42:458-464. [PMID: 33368350 DOI: 10.1002/jcc.26468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/06/2020] [Indexed: 11/07/2022]
Abstract
IOData is a free and open-source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane-wave density-functional-theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand-alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third-party) molecular quantum chemistry and solid-state density-functional-theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.
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Affiliation(s)
- Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium
| | - William Adams
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Leila Pujal
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Alireza Tehrani
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Braden D Kelly
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Luis Macaya
- Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Fanwang Meng
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Michael Richer
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | | | - Xiaotian Derrick Yang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada.,Laboratoire de Chimie Théorique, Sorbonne Université, Paris, France
| | - Matthew Chan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Taewon David Kim
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | | | - Valerii Chuiko
- Faculty of Physics, Taras Shevchenko National University of Kyiv, 01601, Kyiv, Ukraine
| | - Esteban Vöhringer-Martinez
- Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
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