Gerhard Hummer
Max Planck Society
Chemical physicsChemistryMoleculeMolecular dynamicsCrystallography
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Publications 395
#1Jakob Tómas Bullerjahn (MPG: Max Planck Society)H-Index: 1
#2Sören von Bülow (MPG: Max Planck Society)H-Index: 2
Last. Gerhard Hummer (MPG: Max Planck Society)H-Index: 79
view all 3 authors...
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 self-diffusion coefficient and its stati...
1 CitationsSource
#1Sören von Bülow (MPG: Max Planck Society)H-Index: 2
#2Jakob Tómas Bullerjahn (MPG: Max Planck Society)H-Index: 1
Last. Gerhard Hummer (MPG: Max Planck Society)H-Index: 79
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...
1 CitationsSource
#1Ahmad Reza Mehdipour (MPG: Max Planck Society)H-Index: 15
#2Gerhard Hummer (MPG: Max Planck Society)H-Index: 79
Binding of the spike protein of SARS-CoV-2 to the human angiotensin converting enzyme 2 (ACE2) receptor triggers translocation of the virus into cells. Both the ACE2 receptor and the spike protein are heavily glycosylated, including at sites near their binding interface. We built fully glycosylated models of the ACE2 receptor bound to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Using atomistic molecular dynamics (MD) simulations, we found that the glycosylation of the huma...
#1Mateusz Sikora (MPG: Max Planck Society)H-Index: 1
#2Sören von Bülow (MPG: Max Planck Society)H-Index: 2
Last. Gerhard Hummer (Goethe University Frankfurt)H-Index: 79
view all 6 authors...
The severity of the COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, calls for the urgent development of a vaccine. The primary immunological target is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface to mediate viral entry into the host cell. To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully gly...
#1Beata TuroňováH-Index: 2
#2Mateusz Sikora (MPG: Max Planck Society)H-Index: 1
Last. Cindy Hörner (Paul Ehrlich Institute)H-Index: 1
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The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the major focus for vaccine development. We combine cryo electron tomography, subtomogram averaging and molecular dynamics simulations to structurally analyze S in situ. Compared to recombinant S, the viral S is more heavily glycosylated and occurs predominantly in a closed pre-fusion conformation. We show that the stalk domain of S contains three hinges that give the globular ...
1 CitationsSource
#1Sören von Bülow (MPG: Max Planck Society)H-Index: 2
#2Gerhard Hummer (Goethe University Frankfurt)H-Index: 79
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 ...
#1Donghyuk ShinH-Index: 10
Last. Georg TascherH-Index: 2
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1 CitationsSource
#1Alfredo Jost Lopez (MPG: Max Planck Society)H-Index: 1
#2Patrick K. Quoika (MPG: Max Planck Society)
Last. Juergen Koefinger (MPG: Max Planck Society)H-Index: 1
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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: 10
#2Anshu Bhattacharya (Goethe University Frankfurt)
Last. Ivan Dikic (Goethe University Frankfurt)H-Index: 95
view all 9 authors...
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: 3
#2Marc Siggel (MPG: Max Planck Society)H-Index: 2
Last. Tom A. Rapoport (HHMI: Howard Hughes Medical Institute)H-Index: 97
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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...
4 CitationsSource