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Ford MC, Rappé AK, Ho PS. A Reduced Generalized Force Field for Biological Halogen Bonds. J Chem Theory Comput 2021; 17:5369-5378. [PMID: 34232642 DOI: 10.1021/acs.jctc.1c00362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The halogen bond (or X-bond) is a noncovalent interaction that is increasingly recognized as an important design tool for engineering protein-ligand interactions and controlling the structures of proteins and nucleic acids. In the past decade, there have been significant efforts to characterize the structure-energy relationships of this interaction in macromolecules. Progress in the computational modeling of X-bonds in biological molecules, however, has lagged behind these experimental studies, with most molecular mechanics/dynamics-based simulation methods not properly treating the properties of the X-bond. We had previously derived a force field for biological X-bonds (ffBXB) based on a set of potential energy functions that describe the anisotropic electrostatic and shape properties of halogens participating in X-bonds. Although fairly accurate for reproducing the energies within biomolecular systems, including X-bonds engineered into a DNA junction, the ffBXB with its seven variable parameters was considered to be too unwieldy for general applications. In the current study, we have generalized the ffBXB by reducing the number of variables to just one for each halogen type and show that this remaining electrostatic variable can be estimated for any new halogenated molecule through a standard restricted electrostatic potential calculation of atomic charges. In addition, we have generalized the ffBXB for both nucleic acids and proteins. As a proof of principle, we have parameterized this reduced and more general ffBXB against the AMBER force field. The resulting parameter set was shown to accurately recapitulate the quantum mechanical landscape and experimental interaction energies of X-bonds incorporated into DNA junction and T4 lysozyme model systems. Thus, this reduced and generalized ffBXB is more readily adaptable for incorporation into classical molecular mechanics/dynamics algorithms, including those commonly used to design inhibitors against therapeutic targets in medicinal chemistry and materials in biomolecular engineering.
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Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Anthony K Rappé
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
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2
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Czarny RS, Ho AN, Shing Ho P. A Biological Take on Halogen Bonding and Other Non-Classical Non-Covalent Interactions. CHEM REC 2021; 21:1240-1251. [PMID: 33886153 DOI: 10.1002/tcr.202100076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/07/2021] [Indexed: 01/23/2023]
Abstract
Classical hydrogen bonds have, for many decades, been the dominant non-covalent interaction in the toolbox that chemists and chemical engineers have used to design and control the structures of compounds and molecular assemblies as novel materials. Recently, a set of non-classical non-covalent (NC-NC) interactions have emerged that exploit the properties of the Group IV, V, VI, and VII elements of the periodic table (the tetrel, pnictogen, chalcogen, and halogen bonds, respectively). Our research group has been characterizing the prevalence, geometric constraints, and structure-function relationship specifically of the halogen bond in biological systems. We have been particularly interested in exploiting the biological halogen bonds (or BXBs) to control the structures, stabilities, and activities of biomolecules, including the DNA Holliday junction and enzymes. In this review, we first provide a set of criteria for how to determine whether BXBs or any other NC-NC interactions would have biological relevance. We then navigate the trail of studies that had led us from an initial, very biological question to our current point in the journey to establish BXBs as a tool for biomolecular engineering. Finally, we close with a perspective on future directions for this line of research.
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Affiliation(s)
- Ryan S Czarny
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - Alexander N Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
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3
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Pizzi A, Pigliacelli C, Bergamaschi G, Gori A, Metrangolo P. Biomimetic engineering of the molecular recognition and self-assembly of peptides and proteins via halogenation. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213242] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Carlsson ACC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds. Biochemistry 2018; 57:4135-4147. [PMID: 29921126 PMCID: PMC6052408 DOI: 10.1021/acs.biochem.8b00603] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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The construction of more stable proteins
is important in biomolecular
engineering, particularly in the design of biologics-based therapeutics.
We show here that replacing the tyrosine at position 18 (Y18) of T4
lysozyme with the unnatural amino acid m-chlorotyrosine
(mClY) increases both the thermal stability
(increasing the melting temperature by ∼1 °C and the melting
enthalpy by 3 kcal/mol) and the enzymatic activity at elevated temperatures
(15% higher than that of the parent enzyme at 40 °C) of this
classic enzyme. The chlorine of mClY forms
a halogen bond (XB) to the carbonyl oxygen of the peptide bond at
glycine 28 (G28) in a tight loop near the active site. In this case,
the XB potential of the typically weak XB donor Cl is shown from quantum
chemical calculations to be significantly enhanced by polarization
via an intramolecular hydrogen bond (HB) from the adjacent hydroxyl
substituent of the tyrosyl side chain, resulting in a distinctive
synergistic HB-enhanced XB (or HeX-B for short) interaction. The larger
halogens (bromine and iodine) are not well accommodated within this
same loop and, consequently, do not exhibit the effects on protein
stability or function associated with the HeX-B interaction. Thus,
we have for the first time demonstrated that an XB can be engineered
to stabilize and increase the activity of an enzyme, with the increased
stabilizing potential of the HeX-B further extending the application
of halogenated amino acids in the design of more stable protein therapeutics.
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Affiliation(s)
- Anna-Carin C Carlsson
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Matthew R Scholfield
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Rhianon K Rowe
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Melissa Coates Ford
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Austin T Alexander
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - Ryan A Mehl
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
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5
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Abstract
The halogen bond (X-bond) has become an important design element in chemistry, including medicinal chemistry and biomolecular engineering. Although oxygen is the most prevalent and best characterized X-bond acceptor in biomolecules, the interaction is seen with nitrogen, sulfur, and aromatic systems as well. In this study, we characterize the structure and thermodynamics of a Br···S X-bond between a 5-bromouracil base and a phosphorothioate in a model DNA junction. The single-crystal structure of the junction shows the geometry of the Br···S to be variable, while calorimetric studies show that the anionic S acceptor is comparable to or slightly more stable than the analogous O acceptor, with a -3.5 kcal/mol difference in ΔΔH25°C and -0.4 kcal/mol ΔΔG25°C (including an entropic penalty ΔΔS25°C of -10 cal/(mol K)). Thus sulfur is shown to be a favorable acceptor for bromine X-bonds, extending the application of this interaction for the design of inhibitors and biological materials.
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Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
| | - Matthew Saxton
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
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Scholfield MR, Ford MC, Carlsson ACC, Butta H, Mehl RA, Ho PS. Structure–Energy Relationships of Halogen Bonds in Proteins. Biochemistry 2017; 56:2794-2802. [DOI: 10.1021/acs.biochem.7b00022] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew R. Scholfield
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Anna-Carin C. Carlsson
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Hawera Butta
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
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7
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Rowe RK, Ho PS. Relationships between hydrogen bonds and halogen bonds in biological systems. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:255-264. [PMID: 28362290 DOI: 10.1107/s2052520617003109] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.
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Affiliation(s)
- Rhianon K Rowe
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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8
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Vander Zanden CM, Rowe RK, Broad AJ, Robertson AB, Ho PS. Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions. Biochemistry 2016; 55:5781-5789. [PMID: 27653243 PMCID: PMC5258817 DOI: 10.1021/acs.biochem.6b00801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
5-Hydroxymethylcytosine (5hmC) is an epigenetic marker that has recently been shown to promote homologous recombination (HR). In this study, we determine the effects of 5hmC on the structure, thermodynamics, and conformational dynamics of the Holliday junction (the four-stranded DNA intermediate associated with HR) in its native stacked-X form. The hydroxymethyl and the control methyl substituents are placed in the context of an amphimorphic GxCC trinucleotide core sequence (where xC is C, 5hmC, or the methylated 5mC), which is part of a sequence also recognized by endonuclease G to promote HR. The hydroxymethyl group of the 5hmC junction adopts two distinct rotational conformations, with an in-base-plane form being dominant over the competing out-of-plane rotamer that has typically been seen in duplex structures. The in-plane rotamer is seen to be stabilized by a more stable intramolecular hydrogen bond to the junction backbone. Stabilizing hydrogen bonds (H-bonds) formed by the hydroxyl substituent in 5hmC or from a bridging water in the 5mC structure provide approximately 1.5-2 kcal/mol per interaction of stability to the junction, which is mostly offset by entropy compensation, thereby leaving the overall stability of the G5hmCC and G5mCC constructs similar to that of the GCC core. Thus, both methyl and hydroxymethyl modifications are accommodated without disrupting the structure or stability of the Holliday junction. Both 5hmC and 5mC are shown to open the structure to make the junction core more accessible. The overall consequences of incorporating 5hmC into a DNA junction are thus discussed in the context of the specificity in protein recognition of the hydroxymethyl substituent through direct and indirect readout mechanisms.
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Affiliation(s)
- Crystal M. Vander Zanden
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Rhianon K. Rowe
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Amanda J. Broad
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Adam B. Robertson
- Department of Molecular Microbiology, Sognsvannsveien 20, NO-0027, Oslo University Hospital, Oslo, Norway
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
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9
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Abstract
The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
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Affiliation(s)
- Gabriella Cavallo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Pierangelo Metrangolo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
- VTT-Technical
Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Roberto Milani
- VTT-Technical
Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Tullio Pilati
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Arri Priimagi
- Department
of Chemistry and Bioengineering, Tampere
University of Technology, Korkeakoulunkatu 8, FI-33101 Tampere, Finland
| | - Giuseppe Resnati
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Giancarlo Terraneo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
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10
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Scholfield MR, Ford MC, Vander Zanden CM, Billman MM, Ho PS, Rappé AK. Force Field Model of Periodic Trends in Biomolecular Halogen Bonds. J Phys Chem B 2014; 119:9140-9. [PMID: 25338128 DOI: 10.1021/jp509003r] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The study of the noncovalent interaction now defined as a halogen bond (X-bond) has become one of the fastest growing areas in experimental and theoretical chemistry--its applications as a design tool are highly extensive. The significance of the interaction in biology has only recently been recognized, but has now become important in medicinal chemistry. We had previously derived a set of empirical potential energy functions to model the structure-energy relationships for bromines in biomolecular X-bonds (BXBs). Here, we have extended this force field for BXBs (ffBXB) to the halogens (Cl, Br, and I) that are commonly seen to form stable X-bonds. The ffBXB calculated energies show a remarkable one-to-one linear relationship to explicit BXB energies determined from an experimental DNA junction system, thereby validating the approach and the model. The resulting parameters allow us to interpret the stabilizing effects of BXBs in terms of well-defined physical properties of the halogen atoms, including their size, shape, and charge, showing periodic trends that are predictable along the Group VII column of elements. Consequently, we have established the ffBXB as an accurate computational tool that can be applied, for example, for the design of new therapeutic compounds against clinically important targets and new biomolecular-based materials.
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Affiliation(s)
| | | | | | - M Marie Billman
- ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | | | - Anthony K Rappé
- ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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11
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Abstract
Halogens are atypical elements in biology, but are common as substituents in ligands, including thyroid hormones and inhibitors, which bind specifically to proteins and nucleic acids. The short-range, stabilizing interactions of halogens - now seen as relatively common in biology - conform generally to halogen bonds characterized in small molecule systems and as described by the σ-hole model. The unique properties of biomolecular halogen bonds (BXBs), particularly in their geometric and energetic relationship to classic hydrogen bonds, make them potentially powerful tools for inhibitor design and molecular engineering. This chapter reviews the current research on BXBs, focusing on experimental studies on their structure-energy relationships, how these studies inform the development of computational methods to model BXBs, and considers how BXBs can be applied to the rational design of more effective inhibitors against therapeutic targets and of new biological-based materials.
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Affiliation(s)
- P Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA,
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12
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Shing Ho P, Mergny JL. Nucleic acid structure: a continuing tradition. Methods 2013; 64:1-2. [PMID: 24160748 DOI: 10.1016/j.ymeth.2013.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA.
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