Biomedical subjects

Christian Kandt

Publications and source records attributed to Christian Kandt.

5 recordsLinked to original sources

PubMed2007

Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD.

The nucleotide-induced structural rearrangements in ATP binding cassette (ABC) transporters, leading to substrate translocation, are largely unknown. We have modeled nucleotide binding and release in the vitamin B(12) importer BtuCD using perturbed elastic network calculations and biased molecular dynamics simulations. Both models predict that nucleotide release decreases the tilt between the two transmembrane domains and opens the cytoplasmic gate. Nucleotide binding has the opposite effect. The observed coupling may be relevant for all ABC transporters because of the conservation of nucleotide binding domains and the shared role of ATP in ABC transporters. The rearrangements in the cytoplasmic gate region do not provide enough space for B(12) to diffuse from the transporter pore into the cytoplasm, which could suggest that peristaltic forces are needed to exclude B(12) from the transporter pore.

ATP-Binding Cassette Transporters↗

PubMed2006

Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF.

BtuF is the periplasmic binding protein (PBP) in the vitamin B(12) uptake system in Escherichia coli where it is associated with the ABC transporter BtuCD. When the ligand binds, PBPs generally display large conformational changes, commonly termed the Venus flytrap mechanism. BtuF belongs to a group of PBPs that, on the basis of crystal structures, does not appear to display such behavior. Using 480 ns multicopy molecular dynamics simulations of apo and holo forms of the protein, we investigate the dynamics of BtuF. We find BtuF to be more flexible than previously assumed, displaying clear opening and closing motions which are more pronounced in the apo form. The protein behavior is compatible with a PBP functional model that postulates a closed conformation for the ligand-bound state, whereas the empty form fluctuates between open and closed conformations. Elastic network normal-mode analysis suggests that all BtuF-like PBPs are capable of similar opening and closing motions. It also makes the typical Venus flytrap domain motions a likely common means of how PBP-ABC transporter interaction could occur.

Escherichia coli↗

PubMed2006

Computer simulations of ABC transporter components.

Current computer simulation techniques provide robust tools for studying the detailed structure and functional dynamics of proteins, as well as their interaction with each other and with other biomolecules. In this minireview, we provide an illustration of recent progress and future challenges in computer modeling by discussing computational studies of ATP-binding cassette (ABC) transporters. ABC transporters have multiple components that work in a well coordinated fashion to enable active transport across membranes. The mechanism by which members of this superfamily execute transport remains largely unknown. Molecular dynamics simulations initiated from high-resolution crystal structures of several ABC transporters have proven to be useful in the investigation of the nature of conformational coupling events that may drive transport. In addition, fruitful efforts have been made to predict unknown structures of medically relevant ABC transporters, such as P-glycoprotein, using homology-based computational methods. The various techniques described here are also applicable to gaining an atomically detailed understanding of the functional mechanisms of proteins in general.

ATP-Binding Cassette Transporters↗

PubMed2005

Water dynamics simulation as a tool for probing proton transfer pathways in a heptahelical membrane protein.

The proton transfer pathway in a heptahelical membrane protein, the light-driven proton pump bacteriorhodopsin (BR), is probed by a combined approach of structural analysis of recent X-ray models and molecular dynamics (MD) simulations that provide the diffusion pathways of internal and external water molecules. Analyzing the hydrogen-bond contact frequencies of the water molecules with protein groups, the complete proton pathway through the protein is probed. Beside the well-known proton binding sites in the protein interior-the protonated Schiff base, Asp85 and Asp96, and the H(5)O(2) (+) complex stabilized by Glu204 and Glu194-the proton release and uptake pathways to the protein surfaces are described in great detail. Further residues were identified, by mutation of which the proposed pathways can be verified. In addition the diffusion pathway of water 502 from Lys216 to Asp96 is shown to cover the positions of the intruding waters 503 and 504 in the N-intermediate. The transiently established water chain in the N-state provides a proton pathway from Asp96 to the Schiff base in the M- to N-transition in a Grotthus-like mechanism, as concluded earlier from time-resolved Fourier transform infrared experiments [le Coutre et al., Proc Nat Acad Sci USA 1995;92:4962-4966].

Aspartic Acid↗

PubMed2004

Dynamics of water molecules in the bacteriorhodopsin trimer in explicit lipid/water environment.

Protonated networks of internal water molecules appear to be involved in proton transfer in various integral membrane proteins. High-resolution x-ray studies of protein crystals at low temperature deliver mean positions of most internal waters, but only limited information about fluctuations within such H-bonded networks formed by water and residues. The question arises as to how water molecules behave inside and on the surface of a fluctuating membrane protein under more physiological conditions. Therefore, as an example, long-time molecular dynamics simulations of bacteriorhodopsin were performed with explicit membrane/water environment. Based on a recent x-ray model the bacteriorhodopsin trimer was inserted in a fully solvated 16 x 16 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-bilayer patch, resulting in a system of approximately 84,000 atoms. Unrestrained molecular dynamics calculations of 5 ns were performed using the GROMACS package and force field. Mean water densities were computed to describe the anisotropic distribution of internal water molecules. In the whole protein two larger areas of higher water density are identified. They are located between the central proton binding site, the Schiff base, and the extracellular proton release site. Separated by Arg-82 these water clusters could provide a proton release pathway in a Grotthus-like mechanism as indicated by a continuum absorbance change observed during the photocycle by time-resolved Fourier transform infrared spectroscopy. Residues are identified which are H-bonded to the water clusters and are therefore facilitating proton conduction. Their influence on proton transfer via the H-bonded network as indicated by the continuum absorbance change is predicted. This may explain why several site-directed mutations alter the proton release kinetics without a direct involvement in proton transfer.

Amino Acids↗