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MacKenzie DWS, Schaefer A, Steckner J, Leo CA, Naser D, Artikis E, Broom A, Ko T, Shah P, Ney MQ, Tran E, Smith MTJ, Fuglestad B, Wand AJ, Brooks CL, Meiering EM. A fine balance of hydrophobic-electrostatic communication pathways in a pH-switching protein. Proc Natl Acad Sci U S A 2022; 119:e2119686119. [PMID: 35737838 PMCID: PMC9245636 DOI: 10.1073/pnas.2119686119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/29/2022] [Indexed: 12/24/2022] Open
Abstract
Allostery is the phenomenon of coupling between distal binding sites in a protein. Such coupling is at the crux of protein function and regulation in a myriad of scenarios, yet determining the molecular mechanisms of coupling networks in proteins remains a major challenge. Here, we report mechanisms governing pH-dependent myristoyl switching in monomeric hisactophilin, whereby the myristoyl moves between a sequestered state, i.e., buried within the core of the protein, to an accessible state, in which the myristoyl has increased accessibility for membrane binding. Measurements of the pH and temperature dependence of amide chemical shifts reveal protein local structural stability and conformational heterogeneity that accompany switching. An analysis of these measurements using a thermodynamic cycle framework shows that myristoyl-proton coupling at the single-residue level exists in a fine balance and extends throughout the protein. Strikingly, small changes in the stereochemistry or size of core and surface hydrophobic residues by point mutations readily break, restore, or tune myristoyl switch energetics. Synthesizing the experimental results with those of molecular dynamics simulations illuminates atomistic details of coupling throughout the protein, featuring a large network of hydrophobic interactions that work in concert with key electrostatic interactions. The simulations were critical for discerning which of the many ionizable residues in hisactophilin are important for switching and identifying the contributions of nonnative interactions in switching. The strategy of using temperature-dependent NMR presented here offers a powerful, widely applicable way to elucidate the molecular mechanisms of allostery in proteins at high resolution.
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Affiliation(s)
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Julia Steckner
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Christopher A. Leo
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Efrosini Artikis
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - Aron Broom
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Travis Ko
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Purnank Shah
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Mikaela Q. Ney
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Elisa Tran
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Martin T. J. Smith
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Brian Fuglestad
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - A. Joshua Wand
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Charles L. Brooks
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109
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Gupta PL, Smith JS, Roitberg AE. pH Effects and Cooperativity among Key Titratable Residues for Escherichia coli Glycinamide Ribonucleotide Transformylase. J Phys Chem B 2021; 125:9168-9185. [PMID: 34351775 DOI: 10.1021/acs.jpcb.1c04668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Human glycinamide ribonucleotide transformylase (GAR Tfase) is a regulatory enzyme in the de novo purine biosynthesis pathway that has been extensively studied as an anticancer target. To some extent, inhibition of GAR Tfase selectively targets cancer cells over normal cells and inhibits purine formation and DNA replication. In this study, we investigated E. coli GAR Tfase, which shares high sequence similarity with the human GAR Tfase, and most functional residues are conserved. Herein, we aim to predict the pH-activity curve through a computational approach. We carried out pH-replica exchange molecular dynamics (pH-REMD) simulations to investigate pH-dependent functions such as structural changes, ligand binding, and catalytic activity. To compute the pH-activity curve, we identified the catalytic residues in specific protonation states, referred to as the catalytic competent protonation states (CCPS), which maintain the structure, keep ligands bound, and facilitate catalysis. Our computed population of CCPS with respect to pH matches well with the experimental pH-activity curve. To compute the microscopic pKa values in the catalytically active conformation, we devised a thermodynamic model that considers the coupling between protonation states of CCPS residues and conformational states. These results allow us to correctly identify the general acid and base catalysts and interpret the pH-activity curve at an atomistic level.
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Affiliation(s)
- Pancham Lal Gupta
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Justin S Smith
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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Nonnative interactions regulate folding and switching of myristoylated protein. Proc Natl Acad Sci U S A 2012; 109:17839-44. [PMID: 22847411 DOI: 10.1073/pnas.1201803109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present an integrated experimental and computational study of the molecular mechanisms by which myristoylation affects protein folding and function, which has been little characterized to date. Myristoylation, the covalent linkage of a hydrophobic C14 fatty acyl chain to the N-terminal glycine in a protein, is a common modification that plays a critical role in vital regulated cellular processes by undergoing reversible energetic and conformational switching. Coarse-grained folding simulations for the model pH-dependent actin- and membrane-binding protein hisactophilin reveal that nonnative hydrophobic interactions of the myristoyl with the protein as well as nonnative electrostatic interactions have a pronounced effect on folding rates and thermodynamic stability. Folding measurements for hydrophobic residue mutations of hisactophilin and atomistic simulations indicate that the nonnative interactions of the myristoyl group in the folding transition state are nonspecific and robust, and so smooth the energy landscape for folding. In contrast, myristoyl interactions in the native state are highly specific and tuned for sensitive control of switching functionality. Simulations and amide hydrogen exchange measurements provide evidence for increases as well as decreases in stability localized on one side of the myristoyl binding pocket in the protein, implicating strain and altered dynamics in switching. The effects of folding and function arising from myristoylation are profoundly different from the effects of other post-translational modifications.
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Murtaugh ML, Fanning SW, Sharma TM, Terry AM, Horn JR. A combinatorial histidine scanning library approach to engineer highly pH-dependent protein switches. Protein Sci 2011; 20:1619-31. [PMID: 21766385 DOI: 10.1002/pro.696] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 07/07/2011] [Indexed: 12/17/2022]
Abstract
There is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein-protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton-linkage dictate that the presence of multiple ionizable groups, which undergo a pK(a) change on protein binding, are necessary to result in highly pH-dependent binding. To test this hypothesis, a novel combinatorial histidine library was developed where every possible combination of histidine and wild-type residue is sampled throughout the interface of a model anti-RNase A single domain VHH antibody. Antibodies were coselected for high-affinity binding and pH-sensitivity using an in vitro, dual-function selection strategy. The resulting antibodies retained near wild-type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine "hot-spots," which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH-sensitive protein affinity reagents for a number of different applications.
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Affiliation(s)
- Megan L Murtaugh
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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