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Kasson, P. M.
Alternative names
Publications (10 of 14) Show all publications
Ferreira, R. J. & Kasson, P. M. (2019). Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics. ACS INFECTIOUS DISEASES, 5(12), 2096-2104
Open this publication in new window or tab >>Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics
2019 (English)In: ACS INFECTIOUS DISEASES, ISSN 2373-8227, Vol. 5, no 12, p. 2096-2104Article in journal (Refereed) Published
Abstract [en]

Crossing the Gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay of outer membrane vesicle swelling. Parallel molecular dynamics simulations of compound uptake through Escherichia coli (E. coli) OmpF are used to successfully and quantitatively predict experimental permeabilities measured via either outer membrane swelling or prior liposome-swelling measurements. These simulations are analyzed using an inhomogeneous solubility-diffusion model to yield predictions of permeability. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer membrane permeability.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2019
Keywords
outer membrane vesicles, molecular dynamics simulation, outer membrane porins, membrane permeability
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-402242 (URN)10.1021/acsinfecdis.9b00201 (DOI)000503114600016 ()31593635 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation
Available from: 2020-01-16 Created: 2020-01-16 Last updated: 2020-01-16Bibliographically approved
Rawle, R. J., Giraldo, A. M. V., Boxer, S. G. & Kasson, P. M. (2019). Detecting and Controlling Dye Effects in Single-Virus Fusion Experiments. Biophysical Journal, 117(3), 445-452
Open this publication in new window or tab >>Detecting and Controlling Dye Effects in Single-Virus Fusion Experiments
2019 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 117, no 3, p. 445-452Article in journal (Refereed) Published
Abstract [en]

Fluorescent dye-dequenching assays provide a powerful and versatile means to monitor membrane fusion events. They have been used in bulk assays, for measuring single events in live cells, and for detailed analysis of fusion kinetics for liposomal, viral, and cellular fusion processes; however, the dyes used also have the potential to perturb membrane fusion. Here, using single-virus measurements of influenza membrane fusion, we show that fluorescent membrane probes can alter both the efficiency and the kinetics of lipid mixing in a dye- and illumination-dependent manner. R18, a dye that is commonly used to monitor lipid mixing between membranes, is particularly prone to these effects, whereas Texas Red is somewhat less sensitive. R18 further undergoes photoconjugation to viral proteins in an illumination-dependent manner that correlates with its inactivation of viral fusion. These results demonstrate how fluorescent probes can perturb measurements of biological activity and provide both data and a method for determining minimally perturbative measurement conditions.

Place, publisher, year, edition, pages
CELL PRESS, 2019
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-393335 (URN)10.1016/j.bpj.2019.06.022 (DOI)000478966500005 ()31326109 (PubMedID)
Funder
Wallenberg FoundationsNIH (National Institute of Health), R35 GM118044NIH (National Institute of Health), R01 GM098304
Available from: 2019-09-27 Created: 2019-09-27 Last updated: 2019-09-27Bibliographically approved
Hays, J. M., Cafiso, D. S. & Kasson, P. M. (2019). Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data. Journal of Physical Chemistry Letters, 10(12), 3410-3414
Open this publication in new window or tab >>Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data
2019 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 12, p. 3410-3414Article in journal (Refereed) Published
Abstract [en]

Multistructured biomolecular systems play crucial roles in a wide variety of cellular processes but have resisted traditional methods of structure determination, which often resolve only a few low-energy states. High-resolution structure determination using experimental methods that yield distributional data remains extremely difficult, especially when the underlying conformational ensembles are quite heterogeneous. We have therefore developed a method to integrate sparse, multimultimodal spectroscopic data to obtain high-resolution estimates of conformational ensembles. We have tested our method by incorporating double electron-electron resonance data on the soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) protein syntaxin-1a into biased molecular dynamics simulations. We find that our method substantially outperforms existing state-of-the-art methods in capturing syntaxins open-closed conformational equilibrium and further yields new conformational states that are consistent with experimental data and may help in understanding syntaxin's function. Our improved methods for refining heterogeneous conformational ensembles from spectroscopic data will greatly accelerate the structural understanding of such systems.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2019
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-390681 (URN)10.1021/acs.jpclett.9b01407 (DOI)000472804700034 ()31181934 (PubMedID)
Available from: 2019-08-15 Created: 2019-08-15 Last updated: 2019-08-15Bibliographically approved
Liao, Q., Lüking, M., Krueger, D. M., Deindl, S., Elf, J., Kasson, P. M. & Kamerlin, S. C. (2019). Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition. Journal of Physical Chemistry B, 123(17), 3576-3590
Open this publication in new window or tab >>Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition
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2019 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, no 17, p. 3576-3590Article in journal (Refereed) Published
Abstract [en]

Recent years have witnessed an explosion of interest in computational studies of DNA binding proteins, including both coarse grained and atomistic simulations of transcription factor-DNA recognition, to understand how these transcription factors recognize their binding sites on the DNA with such exquisite specificity. The present study performs microsecond time scale all-atom simulations of the dimeric form of the lactose repressor (Lad), both in the absence of any DNA and in the presence of both specific and nonspecific complexes, considering three different DNA sequences. We examine, specifically, the conformational differences between specific and nonspecific protein DNA interactions, as well as the behavior of the helix-turn-helix motif of Lad when interacting with the DNA. Our simulations suggest that stable Lad binding occurs primarily to bent A-form DNA, with a loss of Lad conformational entropy and optimization of correlated conformational equilibria across the protein. In addition, binding to the specific operator sequence involves a slightly larger number of stabilizing DNA protein hydrogen bonds (in comparison to nonspecific complexes), which may account for the experimentally observed specificity for this operator. In doing so, our simulations provide a detailed atomistic description of potential structural drivers for LacI selectivity.

National Category
Physical Chemistry Biophysics
Identifiers
urn:nbn:se:uu:diva-384077 (URN)10.1021/acs.jpcb.8b12363 (DOI)000466989000003 ()30952192 (PubMedID)
Funder
Swedish Research Council, 2016-06213Knut and Alice Wallenberg Foundation, KAW 2016.0077
Available from: 2019-05-28 Created: 2019-05-28 Last updated: 2020-01-30Bibliographically approved
Kasson, P. & Jha, S. (2018). Adaptive ensemble simulations of biomolecules. Current opinion in structural biology, 52, 87-94
Open this publication in new window or tab >>Adaptive ensemble simulations of biomolecules
2018 (English)In: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 52, p. 87-94Article in journal (Refereed) Published
Abstract [en]

Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of individual simulation trajectories and analyze statistics across them. Adaptive ensemble simulations offer a further level of sophistication and flexibility by enabling high-level algorithms to control simulations-based on intermediate results. We review some of the adaptive ensemble algorithms and software infrastructure currently in use and outline where the complexities of implementing adaptive simulation have limited algorithmic innovation to date. We describe an adaptive ensemble API to overcome some of these barriers and more flexibly and simply express adaptive simulation algorithms to help realize the power of this type of simulation.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-365008 (URN)10.1016/j.sbi.2018.09.005 (DOI)000455065800013 ()30265901 (PubMedID)
Funder
NIH (National Institute of Health), R01 GM115790
Available from: 2018-11-07 Created: 2018-11-07 Last updated: 2019-01-25Bibliographically approved
Goronzy, I. N., Rawle, R. J., Boxer, S. G. & Kasson, P. M. (2018). Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering. Chemical Science, 9(8), 2340-2347
Open this publication in new window or tab >>Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering
2018 (English)In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 8, p. 2340-2347Article in journal (Refereed) Published
Abstract [en]

Influenza virus infects cells by binding to sialylated glycans on the cell surface. While the chemical structure of these glycans determines hemagglutinin-glycan binding affinity, bimolecular affinities are weak, so binding is avidity-dominated and driven by multivalent interactions. Here, we show that membrane spatial organization can control viral binding. Using single-virus fluorescence microscopy, we demonstrate that the sterol composition of the target membrane enhances viral binding avidity in a dose-dependent manner. Binding shows a cooperative dependence on concentration of receptors for influenza virus, as would be expected for a multivalent interaction. Surprisingly, the ability of sterols to promote viral binding is independent of their ability to support liquid-liquid phase separation in model systems. We develop a molecular explanation for this observation via molecular dynamics simulations, where we find that cholesterol promotes small-scale clusters of glycosphingolipid receptors. We propose a model whereby cholesterol orders the monomeric state of glycosphingolipid receptors, reducing the entropic penalty of receptor association and thus favoring multimeric complexes without phase separation. This model explains how cholesterol and other sterols control the spatial organization of membrane receptors for influenza and increase viral binding avidity. A natural consequence of this finding is that local cholesterol concentration in the plasma membrane of cells may alter the binding avidity of influenza virions. Furthermore, our results demonstrate a form of cholesterol-dependent membrane organization that does not involve lipid rafts, suggesting that cholesterol's effect on cell membrane heterogeneity is likely the interplay of several different factors.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2018
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-351012 (URN)10.1039/c7sc03236f (DOI)000427091500031 ()29520318 (PubMedID)
Funder
Wallenberg FoundationsNIH (National Institute of Health), R01 GM098304NIH (National Institute of Health), R35 GM118044
Available from: 2018-05-24 Created: 2018-05-24 Last updated: 2018-05-24Bibliographically approved
Cortina, G. A., Hays, J. M. & Kasson, P. M. (2018). Conformational Intermediate That Controls KPC-2 Catalysis and Beta-Lactam Drug Resistance. ACS Catalysis, 8(4), 2741-2747
Open this publication in new window or tab >>Conformational Intermediate That Controls KPC-2 Catalysis and Beta-Lactam Drug Resistance
2018 (English)In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 8, no 4, p. 2741-2747Article in journal (Refereed) Published
Abstract [en]

The KPC-2 carbapenemase enzyme is responsible for drug resistance in the majority of carbapenem-resistant Gram-negative bacterial infections in the United States. A better understanding of what permits KPC-2 to hydrolyze carbapenem antibiotics and how this might be inhibited is thus of fundamental interest and great practical importance to development of better anti-infectives. By correlating molecular dynamics simulations with experimental enzyme kinetics, we identified conformational changes that control KPC-2's ability to hydrolyze carbapenem antibiotics. Related beta-lactamase enzymes can interconvert between catalytically permissive and catalytically nonpermissive forms of an acylenzyme intermediate critical to drug hydrolysis. identify a similar equilibrium in KPC-2 and analyze the determinants of this conformational change. Because the conformational dynamics of KPC-2 are complex and sensitive to allosteric changes, we develop an information-theoretic approach to identify key determinants of this change. We measure unbiased estimators of the reaction coordinate between catalytically permissive and nonpermissive states, perform information-theoretic feature selection, and, using restrained molecular dynamics simulations, validate the protein conformational changes predicted to control catalytically permissive geometry. We identify two binding pocket residues that control the conformational transitions between catalytically active and inactive forms of KPC-2. Mutations to one of these residues, Trp105, lower the stability of the catalytically permissive state in simulations and have reduced experimental k(cat) values that show a strong linear correlation with the simulated catalytically permissive state lifetimes. This understanding can be leveraged to predict the drug resistance of further KPC-2 mutants and help design inhibitors to combat extreme drug resistance.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
Keywords
catalytic intermediate, off-pathway, molecular dynamics simulation, beta-lactamase, committor analysis, KPC-2
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-356326 (URN)10.1021/acscatal.7b03832 (DOI)000430154100014 ()
Available from: 2018-07-26 Created: 2018-07-26 Last updated: 2018-07-26Bibliographically approved
Irrgang, M. E., Hays, J. M. & Kasson, P. M. (2018). gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.. Bioinformatics
Open this publication in new window or tab >>gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.
2018 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811Article in journal (Refereed) Epub ahead of print
Abstract [en]

Summary: Molecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are implementing custom interactions, for instance biases derived from experimental data, and running ensembles of simulations. We present a Python high-level interface for the popular simulation package GROMACS that 1) allows custom potential functions without modifying the simulation package code, 2) maintains the optimized performance of GROMACS, and 3) presents an abstract interface to building and executing computational graphs that allows transparent low-level optimization of data flow and task placement. Minimal dependencies make this integrated API for the GROMACS simulation engine simple, portable, and maintainable. We demonstrate this API for experimentally-driven refinement of protein conformational ensembles.

Availability: LGPLv2.1 source and instructions are available at https://github.com/kassonlab/gmxapi.

Supplementary information: Supplementary data are available at Bioinformatics online.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-365010 (URN)10.1093/bioinformatics/bty484 (DOI)29912282 (PubMedID)
Available from: 2018-11-07 Created: 2018-11-07 Last updated: 2018-11-12Bibliographically approved
Zawada, K. E., Okamoto, K. & Kasson, P. M. (2018). Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Journal of Molecular Biology, 430(5), 594-601
Open this publication in new window or tab >>Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion
2018 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 430, no 5, p. 594-601Article in journal (Refereed) Published
Abstract [en]

Influenza viral entry into the host cell cytoplasm is accomplished by a process of membrane fusion mediated by the viral hemagglutinin protein. Hem agglutinin acts in a pH-triggered fashion, inserting a short fusion peptide into the host membrane followed by refolding of a coiled-coil structure to draw the viral envelope and host membranes together. Mutations to this fusion peptide provide an important window into viral fusion mechanisms and protein-membrane interactions. Here, we show that a well-described fusion peptide mutant, G1S, has a phenotype that depends strongly on the viral membrane context. The G1S mutant is well known to cause a "hemifusion" phenotype based on experiments in transfected cells, where cells expressing G1S hemagglutinin can undergo lipid mixing in a pH triggered fashion similar to virus but will not support fusion pores. We compare fusion by the G1S hemagglutinin mutant expressed either in cells or in influenza virions and show that this hemifusion phenotype occurs in transfected cells but that native virions are able to support full fusion, albeit at a slower rate and 10-100x reduced infectious titer. We explain this with a quantitative model where the G1S mutant, instead of causing an absolute block of fusion, alters the protein stoichiometry required for fusion. This change slightly slows fusion at high hemagglutinin density, as on the viral surface, but at lower hemagglutinin density produces a hemifusion phenotype. The quantitative model thus reproduces the observed virus-cell and cell-cell fusion phenotypes, yielding a unified explanation where membrane context can control the observed viral fusion phenotype. (C) 2018 Elsevier Ltd. All rights reserved.

Place, publisher, year, edition, pages
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2018
Keywords
influenza virus, membrane fusion, fusion peptide, stoichiometry, hemifusion
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-352730 (URN)10.1016/j.jmb.2018.01.006 (DOI)000429398200004 ()29355500 (PubMedID)
Available from: 2018-06-07 Created: 2018-06-07 Last updated: 2018-06-07Bibliographically approved
Rawle, R. J., Webster, E. R., Jelen, M., Kasson, P. M. & Boxer, S. G. (2018). pH Dependence of Zika Membrane Fusion Kinetics Reveals an Off-Pathway State. ACS CENTRAL SCIENCE, 4(11), 1503-1510
Open this publication in new window or tab >>pH Dependence of Zika Membrane Fusion Kinetics Reveals an Off-Pathway State
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2018 (English)In: ACS CENTRAL SCIENCE, ISSN 2374-7943, Vol. 4, no 11, p. 1503-1510Article in journal (Refereed) Published
Abstract [en]

The recent spread of Zika virus stimulated extensive research on its structure, pathogenesis, and immunology, but mechanistic study of entry has lagged behind, in part due to the lack of a defined reconstituted system. Here, we report Zika membrane fusion measured using a platform that bypasses these barriers, enabling observation of single-virus fusion kinetics without receptor reconstitution. Surprisingly, target membrane binding and low pH are sufficient to trigger viral hemifusion to liposomes containing only neutral lipids. Second, although the extent of hemifusion strongly depends on pH, hemifusion rates are relatively insensitive to pH. Kinetic analysis shows that an off-pathway state is required to capture this pH-dependence and suggests this may be related to viral inactivation. Our surrogate-receptor approach thus yields new understanding of flaviviral entry mechanisms and should be applicable to many emerging viruses.

National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-372442 (URN)10.1021/acscentsci.8b00494 (DOI)000451524400009 ()
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07Bibliographically approved
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