1
|
Gentile R, Modric M, Thiele B, Jaeger KE, Kovacic F, Schott-Verdugo S, Gohlke H. Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-Regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa. JACS AU 2024; 4:958-973. [PMID: 38559719 PMCID: PMC10976570 DOI: 10.1021/jacsau.3c00725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 04/04/2024]
Abstract
PlaF is a membrane-bound phospholipase A1 from Pseudomonas aeruginosa that is involved in remodeling membrane glycerophospholipids (GPLs) and modulating virulence-associated signaling and metabolic pathways. Previously, we identified the role of medium-chain free fatty acids (FFAs) in inhibiting PlaF activity and promoting homodimerization, yet the underlying molecular mechanism remained elusive. Here, we used unbiased and biased molecular dynamics simulations and free energy computations to assess how PlaF interacts with FFAs localized in the water milieu surrounding the bilayer or within the bilayer and how these interactions regulate PlaF activity. Medium-chain FFAs localized in the upper bilayer leaflet can stabilize inactive dimeric PlaF, likely through interactions with charged surface residues, as has been experimentally validated. Potential of mean force (PMF) computations indicate that membrane-bound FFAs may facilitate the activation of monomeric PlaF by lowering the activation barrier for changing into a tilted, active configuration. We estimated that the coupled equilibria of PlaF monomerization-dimerization and tilting at the physiological concentration of PlaF lead to the majority of PlaF forming inactive dimers when in a cell membrane loaded with decanoic acid (C10). This is in agreement with a suggested in vivo product feedback loop and gas chromatography-mass spectrometry profiling results, indicating that PlaF catalyzes the release of C10 from P. aeruginosa membranes. Additionally, we found that C10 in the water milieu can access the catalytic site of active monomeric PlaF, contributing to the competitive component of C10-mediated PlaF inhibition. Our study provides mechanistic insights into how medium-chain FFAs may regulate the activity of PlaF, a potential bacterial drug target.
Collapse
Affiliation(s)
- Rocco Gentile
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Matea Modric
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
| | - Björn Thiele
- Institute
of Bio- and Geosciences (IBG-2: Plant Sciences and IBG-3: Agrosphere), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
- Institute
of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Filip Kovacic
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
| | - Stephan Schott-Verdugo
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| |
Collapse
|
2
|
Brumett R, Danai L, Coffman A, Radwan Y, Teter M, Hayth H, Doe E, Pranger K, Thornburgh S, Dittmer A, Li Z, Kim TJ, Afonin KA, Khisamutdinov EF. Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications. Biochemistry 2024; 63:312-325. [PMID: 38271599 DOI: 10.1021/acs.biochem.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We report a thorough investigation of the role of single-stranded thymidine (ssT) linkers in the stability and flexibility of minimal, multistranded DNA nanostructures. We systematically explore the impact of varying the number of ssTs in three-way junction motifs (3WJs) on their formation and properties. Through various UV melting experiments and molecular dynamics simulations, we demonstrate that while the number of ssTs minimally affects thermodynamic stability, the increasing ssT regions significantly enhance the structural flexibility of 3WJs. Utilizing this knowledge, we design triangular DNA nanoparticles with varying ssTs, all showing exceptional assembly efficiency except for the 0T triangle. All triangles demonstrate enhanced stability in blood serum and are nonimmunostimulatory and nontoxic in mammalian cell lines. The 4T 3WJ is chosen as the building block for constructing other polygons due to its enhanced flexibility and favorable physicochemical characteristics, making it a versatile choice for creating cost-effective, stable, and functional DNA nanostructures that can be stored in the dehydrated forms while retaining their structures. Our study provides valuable insights into the design and application of nucleic acid nanostructures, emphasizing the importance of understanding stability and flexibility in the realm of nucleic acid nanotechnology. Our findings suggest the intricate connection between these ssTs and the structural adaptability of DNA 3WJs, paving the way for more precise design and engineering of nucleic acid nanosystems suitable for broad biomedical applications.
Collapse
Affiliation(s)
- Ross Brumett
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Leyla Danai
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Abigail Coffman
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Yasmine Radwan
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Megan Teter
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Katelynn Pranger
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Sable Thornburgh
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Allison Dittmer
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Tae Jin Kim
- Department of Physical Sciences, West Virginia University Institute of Technology, Beckley, West Virginia 25801, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| |
Collapse
|
3
|
Turnbull C, Bones J, Stanley M, Medhavy A, Wang H, Lorenzo AMD, Cappello J, Shanmuganandam S, Pandey A, Seneviratne S, Brown GJ, Meng X, Fulcher D, Burgio G, Man SM, de Lucas Collantes C, Gasior M, López Granados E, Martin P, Jiang SH, Cook MC, Ellyard JI, Athanasopoulos V, Corry B, Canete PF, Vinuesa CG. DECTIN-1: A modifier protein in CTLA-4 haploinsufficiency. SCIENCE ADVANCES 2023; 9:eadi9566. [PMID: 38055819 PMCID: PMC10699772 DOI: 10.1126/sciadv.adi9566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/06/2023] [Indexed: 12/08/2023]
Abstract
Autosomal dominant loss-of-function (LoF) variants in cytotoxic T-lymphocyte associated protein 4 (CTLA4) cause immune dysregulation with autoimmunity, immunodeficiency and lymphoproliferation (IDAIL). Incomplete penetrance and variable expressivity are characteristic of IDAIL caused by CTLA-4 haploinsufficiency (CTLA-4h), pointing to a role for genetic modifiers. Here, we describe an IDAIL proband carrying a maternally inherited pathogenic CTLA4 variant and a paternally inherited rare LoF missense variant in CLEC7A, which encodes for the β-glucan pattern recognition receptor DECTIN-1. The CLEC7A variant led to a loss of DECTIN-1 dimerization and surface expression. Notably, DECTIN-1 stimulation promoted human and mouse regulatory T cell (Treg) differentiation from naïve αβ and γδ T cells, even in the absence of transforming growth factor-β. Consistent with DECTIN-1's Treg-boosting ability, partial DECTIN-1 deficiency exacerbated the Treg defect conferred by CTL4-4h. DECTIN-1/CLEC7A emerges as a modifier gene in CTLA-4h, increasing expressivity of CTLA4 variants and acting in functional epistasis with CTLA-4 to maintain immune homeostasis and tolerance.
Collapse
Affiliation(s)
- Cynthia Turnbull
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Josiah Bones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Maurice Stanley
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Arti Medhavy
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hao Wang
- The Francis Crick Institute, London, UK
| | - Ayla May D. Lorenzo
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jean Cappello
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Somasundhari Shanmuganandam
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Abhimanu Pandey
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sandali Seneviratne
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Grant J Brown
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xiangpeng Meng
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - David Fulcher
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gaetan Burgio
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Si Ming Man
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | | | - Mercedes Gasior
- Hematology Department, Hospital Universitario La Paz, Madrid, Spain
| | - Eduardo López Granados
- Clinical Immunology Department, Hospital Universitario La Paz, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute for Health Research, Madrid, Spain
| | - Pilar Martin
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Centro de Investigacion Biomedica En Rad, Madrid, Spain
| | - Simon H. Jiang
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C. Cook
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Julia I. Ellyard
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Vicki Athanasopoulos
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Pablo F. Canete
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Frazer Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Carola G. Vinuesa
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- The Francis Crick Institute, London, UK
| |
Collapse
|
4
|
Zarzycki P. Distance-dependent dielectric constant at the calcite/electrolyte interface: Implication for surface complexation modeling. J Colloid Interface Sci 2023; 645:752-764. [PMID: 37172485 DOI: 10.1016/j.jcis.2023.04.169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023]
Abstract
HYPOTHESIS The electrical double layer formed at the mineral/electrolyte interface is often modeled using mean-field approaches based on a continuum description of the solvent whose dielectric constant is assumed to decrease monotonically with decreasing distance to the surface. In contrast, molecular simulations show that the solvent polarizability oscillates near the surface similar to the water density profile - as shown previously, for example, by Bonthuis et al. (D.J. Bonthuis, S. Gekle, R.R. Netz, Dielectric Profile of Interfacial Water and its Effect on Double-Layer Capacitance, Phys Rev Lett 107(16) (2011) 166102). We showed that molecular and mesoscale pictures agree by spatially averaging the dielectric constant obtained from molecular dynamics simulations over the distances relevant to the mean-field representation. In addition, the values of capacitances used to describe the electrical double layer in Surface Complexation Models (SCMs) of the mineral/electrolyte interface can be estimated using molecularly informed spatially averaged dielectric constants and positions of hydration layers. EXPERIMENTS First, we used molecular dynamics simulations to model the calcite 101¯4/electrolyte interface. Next, by using atomistic trajectories, we calculated the distance-dependent static dielectric constant and water density in the direction normal to the. Finally, we applied spatial compartmentalization consistent with the model of parallel-plate capacitors connected in series to estimate SCM capacitances. FINDINGS Computationally expensive simulations are required to determine the dielectric constant profile of interfacial water near the mineral surface. On the other hand, water density profiles are readily assessable from much shorter simulation trajectories. Our simulations confirmed that dielectric and water density oscillations at the interface are correlated. Here, we parametrized linear regression models to estimate the dielectric constant directly from the local water density. This is a significant computational shortcut compared to slowly converging calculations relying on total dipole moment fluctuations. The amplitude of the interfacial dielectric constant oscillation can exceed the dielectric constant of the bulk water, suggesting an ice-like frozen state, but only if there are no electrolyte ions. The interfacial accumulation of electrolyte ions causes a decrease in the dielectric constant due to the reduction of water density and re-orientation of water dipoles in ion hydration shells. Finally, we show how to use the computed dielectric properties to estimate SCM's capacitances.
Collapse
Affiliation(s)
- Piotr Zarzycki
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States.
| |
Collapse
|
5
|
Fan K, Zhang Y, Qiu Y, Zhang H. Impacts of targeting different hydration free energy references on the development of ion potentials. Phys Chem Chem Phys 2022; 24:16244-16262. [PMID: 35758314 DOI: 10.1039/d2cp01237e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration free energy (HFE) as the most important solvation parameter is often targeted in ion model development, even though the reported values differ by dozens of kcal mol-1 mainly due to the experimentally undetermined HFE of the proton ΔG°(H+). The choice of ΔG°(H+) obviously affects the hydration of single ions and the relative HFE between the ions with different (magnitude or sign) charges, and the impacts of targeted HFEs on the ion solvation and ion-ion interactions are largely unrevealed. Here we designed point charge models of K+, Mg2+, Al3+, and Cl- ions targeting a variety of HFE references and then investigated the HFE influences on the simulations of dilute and concentrated ion solutions and of the salt ion pairs in gas, liquid, and solid phases. Targeting one more property of ion-water oxygen distances (IOD) leaves the ion-water binding distance invariant, while the binding strength increases with the decreasing (more negative) HFE of ions as a result of a decrease in ΔG°(H+) for the cation and an increase in ΔG°(H+) for the anion. The increase in ΔG°(H+) leads to strengthened cation-anion interactions and thus to close ion-ion contacts, low osmotic pressures, and small activity derivatives in concentrated ion solutions as well as too stable ion pairs of the salts in different phases. The ion diffusivity and water exchange rates around the ions are simply not HFE dependent but rather more complex. Targeting both the aqueous IOD and salt crystal properties of KCl was also attempted and the comparison between different models indicates the complexity and challenge in obtaining a balanced performance between different phases using classical force fields. Our results also support that a real ΔG°(H+) value of -259.8 kcal mol-1 recommended by Hünenberger and Reif guides ion models to reproduce ion-water and ion-ion interactions reasonably at relatively low salt concentrations. Simulations of a metalloprotein show that a relatively more positive ΔG°(H+) for Mg2+ model is better for a reasonable description of the metal binding network.
Collapse
Affiliation(s)
- Kun Fan
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| |
Collapse
|
6
|
Qiu Y, Jiang Y, Zhang Y, Zhang H. Rational Design of Nonbonded Point Charge Models for Monovalent Ions with Lennard-Jones 12-6 Potential. J Phys Chem B 2021; 125:13502-13518. [PMID: 34860517 DOI: 10.1021/acs.jpcb.1c09103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ions are of central importance in nature, and a variety of potential models was proposed to model ions in different phases for an in-depth exploration of ion-related systems. Here, we developed point charge models of 14 monovalent ions with the traditional 12-6 Lennard-Jones (LJ) potential for use in conjunction with 11 water models of TIP3P, OPC3, SPC/E, SPC/Eb, TIP3P-FB, a99SB-disp, TIP4P-Ew, OPC, TIP4P/2005, TIP4P-D, and TIP4P-FB. The designed models reproduced the real hydration free energy (HFE) of ions and the ion-oxygen distance (IOD) in the first hydration shell accurately and simultaneously, a performance similar to the previously reported 12-6-4 LJ-type ion models (12-6 LJ plus an attractive C4 term for cations or a repulsive one for anions). This work, along with our previous work on di-, tri-, and tetravalent metal cations (J. Chem. Inf. Model. 2021, 61, 4031-4044; J. Chem. Inf. Model. 2021, 61, 4613-4629), demonstrates the feasibility of the simple 12-6 LJ potential in ion modeling. In order for the 12-6 LJ potential to reproduce both the HFE and IOD, the LJ R parameters need to be close to Shannon's ionic radii for the highly charged cations and to the Stokes's van der Waals (vdW) radii for the monovalent ions. With an additional C4 term, the R parameters of 12-6-4 LJ ion models agree well with the Stokes's vdW radii and have a more physical meaning. It appears that the C4 term can be merged into the 12-6 LJ potential by a rational tuning of R and the LJ well depth. Simulations of the osmotic coefficients of alkali chloride solutions and the properties of gaseous and solid alkali halides indicate the necessity of further optimizing ion-ion interactions via, for instance, targeting more properties or using a more physical (polarizable) model.
Collapse
Affiliation(s)
- Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| |
Collapse
|