Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo
T Strunk, K Hamacher, F Hoffgaard… - Molecular …, 2011 - Wiley Online Library
Gas vesicles are gas‐filled protein structures increasing the buoyancy of cells. The gas
vesicle envelope is mainly constituted by the 8 kDa protein GvpA forming a wall with a water …
vesicle envelope is mainly constituted by the 8 kDa protein GvpA forming a wall with a water …
Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson–Boltzmann surface area calculations
The objectives of this study include the design of a series of novel fullerene-based inhibitors
for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the …
for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the …
Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features
D Aguilar, B Oliva, C Marino Buslje - PLoS One, 2012 - journals.plos.org
Amino acids committed to a particular function correlate tightly along evolution and tend to
form clusters in the 3D structure of the protein. Consequently, a protein can be seen as a …
form clusters in the 3D structure of the protein. Consequently, a protein can be seen as a …
Understanding HIV-1 protease autoprocessing for novel therapeutic development
L Huang, C Chen - Future medicinal chemistry, 2013 - Taylor & Francis
In the infected cell, HIV-1 protease (PR) is initially synthesized as part of the GagPol
polyprotein. PR autoprocessing is a virus-specific process by which the PR domain …
polyprotein. PR autoprocessing is a virus-specific process by which the PR domain …
A reduced mechanical model for cAMP-modulated gating in HCN channels
We developed an in silico mechanical model to analyze the process of cAMP-induced
conformational modulations in hyperpolarization-activated cyclic nucleotide-gated (HCN) …
conformational modulations in hyperpolarization-activated cyclic nucleotide-gated (HCN) …
Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics
Y Dehouck, AS Mikhailov - PLoS computational biology, 2013 - journals.plos.org
The proper biological functioning of proteins often relies on the occurrence of coordinated
fluctuations around their native structure, or on their ability to perform wider and sometimes …
fluctuations around their native structure, or on their ability to perform wider and sometimes …
Structural organization of DNA in chlorella viruses
T Wulfmeyer, C Polzer, G Hiepler, K Hamacher… - PLoS …, 2012 - journals.plos.org
Chlorella viruses have icosahedral capsids with an internal membrane enclosing their large
dsDNA genomes and associated proteins. Their genomes are packaged in the particles with …
dsDNA genomes and associated proteins. Their genomes are packaged in the particles with …
Estimating sufficient statistics in co-evolutionary analysis by mutual information
P Weil, F Hoffgaard, K Hamacher - Computational biology and chemistry, 2009 - Elsevier
Mutual information (MI) is a standard measure in information theory to observe and quantify
correlated signals and events in both, empirical data sets and theoretical models. In the field …
correlated signals and events in both, empirical data sets and theoretical models. In the field …
Membrane anchoring and interaction between transmembrane domains are crucial for K+ channel function
M Gebhardt, F Hoffgaard, K Hamacher, SM Kast… - Journal of Biological …, 2011 - ASBMB
The small viral channel Kcv is a Kir-like K+ channel of only 94 amino acids. With this simple
structure, the tetramer of Kcv represents the pore module of all complex K+ channels. To …
structure, the tetramer of Kcv represents the pore module of all complex K+ channels. To …
Carbonylhydrazide-based molecular tongs inhibit wild-type and mutated HIV-1 protease dimerization
L Dufau, AS Marques Ressurreição… - Journal of Medicinal …, 2012 - ACS Publications
We have designed and synthesized new molecular tongs based on a rigid naphthalene
scaffold and evaluated their antidimer activity on HIV-1 protease (PR). We inserted …
scaffold and evaluated their antidimer activity on HIV-1 protease (PR). We inserted …