Center for Molecular Modeling - G. Hummer

Dissecting the conformational complexity and mechanism of a bacterial heme transporter

Reza — Wed, 20 Sep 2023 21:39:54 +0000

D. Wu, A. R. Mehdipour, F. Finke, H. G. Goojani, R. R. Groh, T. M. Grund, T. M. B. Reichhart, R. Zimmermann, S. Welsch, D. Bald, M. Shepherd, G. Hummer, S. Safarian

Nature Chemical Biology

19,992–1003

2023

Abstract

Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.

Green Open Access

DOI

http://dx.doi.org/

Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level

Reza — Tue, 27 Dec 2022 10:44:05 +0000

R. Zhu, D. Canena, M. Sikora, M. Klausberger, H. Seferovic, A. R. Mehdipour, L. Hain, E. Laurent, V. Monteil, G. Wirnsberger, R. Wieneke, R. Tampé, N.F. Kienzl, L. Mach, A. Mirazimi, Y. Jin Oh, J.M. Penninger, G. Hummer, P. Hinterdorfer

Nature Communications

13, 7926

2022

Abstract

Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.

DOI

http://dx.doi.org/

Private attachment

s41467-022-35641-3.pdf

Cryo-EM structures of pentameric autoinducer-2 exporter from E. coli reveal its transport mechanism

Reza — Thu, 02 Jun 2022 12:07:47 +0000

R. Khera, A. R. Mehdipour, J.R. Bolla, J. Kahnt, S. Welsch, U. Ermler, C. Muenke, C.V. Robinson, G. Hummer, H. Xie, H. Michel

EMBO Journal

41, 18, e109990

2022

Abstract

Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from E. coli, which belongs to a large underexplored membrane transporter family, the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism. This study emphasizes the structural distinctiveness of this family of pentameric transporters and provides fundamental insights for the ensuing studies.

DOI

http://dx.doi.org/

Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter

Reza — Thu, 02 Jun 2022 09:07:25 +0000

E. Lambert, A. R. Mehdipour, A. Schmidt, G. Hummer, C. Perez

Nature Communications

Volume 13, issue 1, article number 1022

2022

Abstract

Transport of lipids across membranes is fundamental for diverse biological pathways in cells. Multiple ion-coupled transporters take part in lipid translocation, but their mechanisms remain largely unknown. Major facilitator superfamily (MFS) lipid transporters play central roles in cell wall synthesis, brain development and function, lipids recycling, and cell signaling. Recent structures of MFS lipid transporters revealed overlapping architectural features pointing towards a common mechanism. Here we used cysteine disulfide trapping, molecular dynamics simulations, mutagenesis analysis, and transport assays in vitro and in vivo, to investigate the mechanism of LtaA, a proton-dependent MFS lipid transporter essential for lipoteichoic acid synthesis in the pathogen Staphylococcus aureus. We reveal that LtaA displays asymmetric lateral openings with distinct functional relevance and that cycling through outward- and inward-facing conformations is essential for transport activity. We demonstrate that while the entire amphipathic central cavity of LtaA contributes to lipid binding, its hydrophilic pocket dictates substrate specificity. We propose that LtaA catalyzes lipid translocation by a ‘trap-and-flip’ mechanism that might be shared among MFS lipid transporters.

DOI

http://dx.doi.org/10.1038/s41467-022-28361-1

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s41467-022-28361-1.pdf

Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model

wim — Mon, 05 Feb 2018 07:52:29 +0000

O. De Vos, R.M. Venable, T. Van Hecke, G. Hummer, R.W. Pastor, A. Ghysels

Journal of Chemical Theory and Computation (JCTC)

14 (7), 3811-3824

2018

Abstract

The balance of normal and radial (lateral) diffusion of oxygen in phospholipid membranes is critical for biological function. Based on the Smoluchowski equation for the inhomogeneous solubility-diffusion model, Bayesian analysis (BA) can be applied to molecular dynamics trajectories of oxygen to extract the free energy and the normal and radial diffusion profiles. This paper derives a theoretical formalism to convert these profiles into characteristic times and lengths associated with entering, escaping, or completely crossing the membrane. The formalism computes mean first passage times and holds for any process described by rate equations between discrete states. BA of simulations of eight model membranes with varying lipid composition and temperature indicate that oxygen travels 3 to 5 times further in the radial than in the normal direction when crossing the membrane in a time of 15 to 32 ns, thereby confirming the anisotropy of passive oxygen transport in membranes. Moreover, the preceding times and distances estimated from the BA are compared to the aggregate of 280 membrane exits explicitly observed in the trajectories. BA predictions for the distances of oxygen radial diffusion within the membrane are statistically indistinguishable from the corresponding simulation values, yet BA oxygen exit times from the membrane interior are approximately 20% shorter than the simulation values, averaged over seven systems. The comparison supports the BA approach and, therefore, the applicability of the Smoluchowski equation to membrane diffusion. Given the shorter trajectories required for the BA, these results validate the BA as a computationally attractive alternative to direct observation of exits when estimating characteristic times and radial distances. The effect of collective membrane undulations on the BA is also discussed.

DOI

http://dx.doi.org/10.1021/acs.jctc.8b00115

Private attachment

paperII.pdf

Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes

wim — Tue, 26 Sep 2017 13:05:13 +0000

A. Ghysels, R.M. Venable, R.W. Pastor, G. Hummer

Journal of Chemical Theory and Computation (JCTC)

13 (6), 2962-2976

2017

Abstract

A Bayesian-based methodology is developed to estimate diffusion tensors from molecular dynamics simulations of permeants in anisotropic media, and is applied to oxygen in lipid bilayers. By a separation of variables in the Smoluchowski diffusion equation, the multidimensional diffusion is reduced to coupled one-dimensional diffusion problems that are treated by discretization. The resulting diffusivity profiles characterize the membrane transport dynamics as a function of the position across the membrane, discriminating between diffusion normal and parallel to the membrane. The methodology is first validated with neat water, neat hexadecane, and a hexadecane slab surrounded by water, the latter being a simple model for a lipid membrane. Next, a bilayer consisting of pure 1-palmitoyl 2-oleoylphosphatidylcholine (POPC), and a bilayer mimicking the lipid composition of the inner mitochondrial membrane, including cardiolipin, are investigated. We analyze the detailed time evolution of oxygen molecules, in terms of both normal diffusion through and radial diffusion inside the membrane. Diffusion is fast in the more loosely packed interleaflet region, and anisotropic, with oxygen spreading more rapidly in the membrane plane than normal to it. Visualization of the propagator shows that oxygen enters the membrane rapidly, reaching its thermodynamically favored center in about 1 ns, despite the free energy barrier at the headgroup region. Oxygen transport is quantified by computing the oxygen permeability of the membranes and the average radial diffusivity, which confirm the anisotropy of the diffusion. The position-dependent diffusion constants and free energies are used to construct compartmental models and test assumptions used in estimating permeability, including Overtons rule. In particular, a hexadecane slab surrounded by water is found to be a poor model of oxygen transport in membranes because the relevant energy barriers differ substantially.

DOI

http://dx.doi.org/10.1021/acs.ictc.7b00039

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acs.jctc_.7b00039.pdf

Oxygen diffusion water, alkanes, and lipid bilayers

wim — Thu, 11 Apr 2013 07:55:36 +0000

A. Ghysels, R.M. Venable, R.W. Pastor, G. Hummer

COMP 420

ISBN/ISSN:

Talk

Conference / event / venue

ACS Spring Meeting

New Orleans, USA

Sunday, 7 April, 2013 to Thursday, 11 April, 2013

Abstract (private)

talk_ACS.pdf

Conference reference

ACS Spring 2013