Gerhard Hummer
Goethe University Frankfurt
Computational chemistryChemistryMoleculeMolecular dynamicsCrystallography
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Publications 389
#1Sören von Bülow (MPG: Max Planck Society)H-Index: 1
#2Gerhard Hummer (MPG: Max Planck Society)H-Index: 77
The protein Atg2 has been proposed to form a membrane tether that mediates lipid transfer from the ER to the phagophore in autophagy. However, recent kinetic measurements on the human homolog ATG2A indicated a transport rate of only about one lipid per minute, which would be far too slow to deliver the millions of lipids required to form a phagophore on a physiological time scale. Here, we revisit the analysis of the fluorescence quenching experiments. We develop a detailed kinetic model of the ...
The interactions between proteins, nucleic acids, and other macromolecules are essential for their biological functions and shape the physicochemcial properties of the crowded environments inside living cells. Binding interactions are commonly quantified by dissociation constants Kd and both binding and non-binding interactions are quantified by second osmotic virial coefficients B2. As a measure of non-specific binding and stickiness, B2 is receiving renewed attention in the context of so-calle...
#1Donghyuk Shin (Goethe University Frankfurt)H-Index: 7
#2Anshu Bhattacharya (Goethe University Frankfurt)
Last. Ivan Dikic (Goethe University Frankfurt)H-Index: 92
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Legionella pneumophila is a gram-negative pathogenic bacterium that causes Legionaries′ disease. The Legionella genome codes more than 300 effector proteins able to modulate host-pathogen interactions during infection. Among them are also enzymes altering the host-ubiquitination system including bacterial ligases and deubiquitinases. In this study, based on homology-detection screening on 305 Legionella effector proteins, we identified two Legionella OTU-like deubiquitinases (LOT; LotB (Lpg1621/...
#1Xudong Wu (HHMI: Howard Hughes Medical Institute)H-Index: 2
#2Marc Siggel (MPG: Max Planck Society)H-Index: 1
Last. Tom A. Rapoport (HHMI: Howard Hughes Medical Institute)H-Index: 95
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INTRODUCTION Protein homeostasis in the endoplasmic reticulum (ER) is maintained by a quality control system. When a newly synthesized ER protein misfolds, it is ultimately retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome, a pathway referred to as ER-associated protein degradation (ERAD). ERAD alleviates cytotoxic stress imposed by protein misfolding and is implicated in numerous diseases. ERAD is found in all eukaryotic cells but is best studied for the ERAD...
#1Jakob BullerjahnH-Index: 1
#2Sören von BülowH-Index: 1
Last. Gerhard Hummer (MPG: Max Planck Society)H-Index: 77
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Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules. Nonlinearities in MSD curves at short times are handled with a wide variety of ad hoc practices, such as partial and piece-wise fitting of the data. Here, we present a rigorous framework to obtain reliable estimates of the diffusion coefficient and its statistica...
#1Sören von BülowH-Index: 1
#2Jakob BullerjahnH-Index: 1
Last. Gerhard HummerH-Index: 77
view all 3 authors...
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using the Einstein relation, the particle positions need to be unwrapped. Here, we show that a widely used heuristic unwrapping scheme is not suitable for long simulations at constant pressure. Improper accounting for box-volume fluctuations creates, at long times, unphysical trajectories and, in turn, grossly exaggerated diff...
Pore-forming toxins (PFTs) are a diverse class of membrane-active proteins employed primarily by bacteria for unregulated perforation of lipid membranes (1). Based on molecular dynamics (MD) simulations (2), electron cryo-microscopy (cryoEM) structures (3), and atomic force microscopy (AFM) experiments (4), we recently identified two distinct pathways for lipid efflux from large pores (diameter >30 nm) formed by the β-PFT pneumolysin (PLY). Lipids leave the PLY ring laterally upon slow membrane ...
#2Tim N. BalderingH-Index: 1
Last. Marina S. DietzH-Index: 6
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#1Robert ErnstH-Index: 15
#2Roberto CovinoH-Index: 8
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#1Toni RadanovićH-Index: 1
#2Michael GechtH-Index: 1
Last. Robert ErnstH-Index: 15
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