Steric Zipper Peptide Aggregation
We employ molecular dynamics simulations in an explicit solvent environment to
study the spontaneous and induced aggregation of steric zipper peptides at
atomistic detail.
These short model peptides were recently shown to
yield detailed structural insights into aggregates, known as amyloid fibrils, which
are related to life threatening conditions in vivo (e.g. Alzheimers disease).
Our aim is to unveil the energetic and structural determinants that drive the formation of
amyloidogenic peptide assemblies, and also stabilize the formed aggregates.
D. Matthes, V. Gapsys, V. Daebel, B. L. de Groot, Mapping the conformational dynamics and pathways of spontaneous steric zipper peptide oligomerization, PLoS ONE 2011, 6(5): e19129.
Dirk Matthes , Vytautas Gapsys
Automated Free Energy Calculations of Protein-Ligand Complexes
Aim of the project is development of an automated free energy calculations workflow for the protein-ligand complexes. We use "alchemical" method of fast growth thermodynamic integration in combination with molecular dynamics simulations to estimate relative free energies of ligands binding to proteins.
Allostery
Allostery is essential for regulation in many biological systems. In allosteric systems the binding affinity of one binding site depends on the binding in a distant binding site. The information flow between these sites is assumed to be communicated through a conformational change of the system. It is still a challenging question to find this collective motion on an atomistic level. We currently focus on Hemoglobin, ABCE1 and GroEL/ES extracting collective motions from Molecular Dynamics simulations using Principal Component Analysis and related methods.
Nernst-Planck Theory Prediction of Channel Currents
We tested the ability of the Nernst-Planck (NP) theory to accurately predict
channel currents by combining and comparing the results with those of Brownian
dynamics (BD) simulations and molecular dynamics (MD) simulations. The MD
model is shown in the figure. The results showed that the NP theory is
applicable at the microscopic scale. This finding opens a door to utilizing
the results of microscopic simulations in continuum theory which can provide
an efficient way to calculate the ion flux in ion channels. Also, we are
trying to combine MD with BD to establish a more efficient way to simulate not
only the ion flux but also the ion trajectories in ion channels.
Understanding the Molecular Machinery of Aquaporins through Molecular Dynamics Simulations
Aquaporins are protein channels responsible for the permeation of water and
other solutes through biological membranes in response to osmotic
pressure. The main goal is to expand our understanding on the molecular
machinery of aquaporins by employing molecular dynamics simulations and
related computational techniques.
We provide a mechanism for the permeation of solutes through the Plasmodium
falciparum aquaglyceroporin, a promising antimalarial drug target. In this
mechanism, hydrophobic regions in the middle of the channel are the main water
rate limiting barriers. Furthermore, the replacement of water-arginine
interactions and solute-matching at the narrowest region of the channel are
the main determinants underlying selectivity for the permeation of solutes
like glycerol and urea (1).
We also investigate the molecular determinants governing aquaporin gating,
which has emerged as an efficient regulatory mechanism for organisms to
quickly counteract sudden osmotic shocks. Our simulations, together with
structural and functional studies, suggest that the yeast aquaporin-1 may be
gated by both serine phosphorylation or mechanosensing (2). Furthermore, we
observed voltage regulation of the single-channel water permeability of human
AQP1 and AQP4 in silico, attributed to gating transitions of the arginine
residue at the aromatic/arginine region. Our results suggests that voltage
sensitivity may be a general feature of aquaporins, a hypothesis to be tested
experimentally (3).
References:
1. Camilo Aponte-Santamaria, Jochen S. Hub and Bert L. de Groot. Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin. PCCP. 12:10246-10254 (2010).
2. Gerhard Fischer, Urszula Kosinska-Eriksson, Camilo Aponte-Santamaria, Madelene Palmgren, Cecilia Geijer, Kristina Hedfalk, Stefan Hohmann, Bert L. de Groot, Richard Neutze, Karin Lindkvist-Petersson. Crystal Structure of a Yeast Aquaporin at 1.15 Angstrom Reveals a Novel Gating Mechanism. PLoS Biology. 7: e1000130 (2009).
3. Jochen S. Hub, Camilo Aponte-Santamaria, Helmut Grubmüller and Bert L. de Groot. Voltage-regulated water flux through aquaporin channels in silico. Biophys. J. 99:L97-L99 (2010)
Small Compound Interaction with Membrane Channel Proteins
The topic of this project are the interactions of small chemical compounds and
membrane channel proteins. Emphasis is placed on Aquaporins and voltage-gated
potassium channels. Membrane channel proteins steer the acquisition of water
and solutes of cells by facilitating its permeation along their
(electro-)chemical gradients across lipid bilayers. Because of their exposed
position drugs can easily reach these receptors and modify their physiological
function. This is reflected by the fact that more than 50% of novel drugs
modify transmembrane proteins. Therefore, transmembrane channels - a special
kind of membrane proteins - are important for contemporary drug
discovery. However, the experimental screening of thousands of compounds for
the exploration of novel channel blocking compounds is time and cost
intensive.
At the current state, mainly a computational method that is called /molecular docking/has been explored. This method allows the assessment of binding affinities of a large number of compounds in a short time. Because molecular docking algorithms are trained rather on enzymes and globular proteins, we had to benchmark their accuracy on channel like proteins. Molecular docking is acceptable for the exploration of large regions in chemical space, but not accurate enough for the assessment of individual binding affinities. In the future we will apply preferentially computationally more expensive methods for the optimization of compounds that we found.
Hopefully our findings will help to reduce time and costs for future drug development. Our predictions are regularly validated by experimental collaborators in Kiel (Germany), Cambridge (UK) and Aarhus (Denmark). This project is funded by the European Drug Initiative on Channels and Transporters (EDICT).
Ubiquitin Dynamics in Complexes
Protein-protein interactions play an important role in all metabolic
processes. However, the principles underlying these interactions are only
beginning to be understood. Ubiquitin is a small signalling protein that is
covalently attached to proteins to mark them for degradation, regulate
transport or induce other functions. As such, it interacts with and is
recognized by a multitude of binding partners.
We use molecular dynamics simulations to investigate the effect of binding on ubiquitin by comparing simulation ensembles of ubiquitin bound to different binding partners with ensembles of unbound ubiquitin. Both collective structural behaviour and local conformational differences are being considered to identify the principles of ubiquitin binding and determine the influence of complex formation on the dynamic properties of this protein. Particularly the question of induced fit versus conformational selection scenarios both on a global and local level is investigated.
Aquaporins as Gas Channels
Lipid-protein Interactions
In this project we focus on the effect of embedded peptides or proteins on the surrounding membrane and on the effect of the membrane on embedded peptides.
Small peptides involve HIV-1 gp41 or gramicidin like channels. Membrane channel proteins involve VDAC (Voltage Dependent Anion Channel)[1] and Aquaporins.
These systems are being studied in different types of model membranes (DMPC, DPPC, POPE, etc). This work is done with the colaboration of NMR and EPR groups.
[1] Saskia Villinger, Rodolfo Briones, Karin Giller, Ulrich Zachariae, Adam Lange, Bert L. de Groot, Christian Griesinger, Stefan Becker, Markus Zweckstetter. Functional dynamics in the voltage dependent anion channel. Proc. Nat. Acad. Sci. 107: 22546-22551 (2010).
Rodolfo Briones
Nucleotide Affinity and Domain Cooperativity within ABC Proteins
RNase-L Inhibitor, also known as ABCE1, is an ATP Binding Cassette (ABC)
protein which is composed solely of two nucleotide binding domains (NBDs) and
an iron sulfur (FeS) cluster. It was suggested to be associated with various
aspects of protein synthesis, including the binding of translation initiation
factors, translation release factors, export of ribosomal subunits from the
nucleus and ribosome recycling. ABCE1 had been resolved by X-ray in its
ADP-bound conformation only. The two NBDs possess a high structural similarity
between themselves despite that they do not share the same sequence (33%
identity only). Moreover, despite this structural symmetry, ABCE1 has been
reported to be functionally asymmetric, where mutations in one NBD (E238Q,
H269A) reduce its ATP hydrolysis by 30-50% of normal wild type activity, while
the parallel mutations in the second NBD increase it by a 10-fold. Our study
aims revealing the reason for this phenomena, while shedding light on the
structure and mechanism of action of ABC domains. This small and relatively
simple protein which does not interact with any membrane domain as most other
ABC proteins do, constitutes the perfect system to study the inter and intra-
subunit interactions of ABC domains. We intend to examine nucleotide affinity
of the NBDs in different binding conformations, as well as domain dynamics in
the presence of mutations with the goal to understand the source of the
detected functional asymmetry.