Biomedical subjects

Philip C Biggin

Publications and source records attributed to Philip C Biggin.

9 recordsLinked to original sources

PubMed2003

Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein.

Periplasmic binding proteins from Gram-negative bacteria possess a common architecture, comprised of two domains linked by a hinge region, a fold which they share with the neurotransmitter-binding domains of ionotropic glutamate receptors (GluRs). Glutamine-binding protein (GlnBP) is one such protein, whose crystal structure has been solved in both open and closed forms. Multi-nanosecond molecular dynamics simulations have been used to explore motions about the hinge region and how they are altered by ligand binding. Glutamine binding is seen to significantly reduce inter-domain motions about the hinge region. Essential dynamics analysis of inter-domain motion revealed the presence of both hinge-bending and twisting motions, as has been reported for a related sugar-binding protein. Significantly, the influence of the ligand on GlnBP dynamics is similar to that previously observed in simulations of rat glutamate receptor (GluR2) ligand-binding domain. The essential dynamics analysis of GlnBP also revealed a third class of motion which suggests a mechanism for signal transmission in GluRs.

Binding Sites↗

PubMed2003

Extending the structure of an ABC transporter to atomic resolution: modeling and simulation studies of MsbA.

Molecular modeling and simulation approaches have been use to generate a complete model of the prokaryotic ABC transporter MsbA from Escherichia coli, starting from the low-resolution structure-based Calpha trace (PDB code 1JSQ). MsbA is of some biomedical interest as it is homologous to mammalian transporters such as P-glycoprotein and TAP. The quality of the MsbA model is assessed using a combination of molecular dynamics simulations and static structural analysis. These results suggest that the approach adopted for MsbA may be of general utility for generating all atom models from low-resolution crystal structures of membrane proteins. Molecular dynamics simulations of the MsbA model inserted in a fully solvated octane slab (a membrane mimetic environment) reveal that while the monomer is relatively stable, the dimer is unstable and undergoes significant conformational drift on a nanosecond time scale. This suggests that the MsbA crystal dimer may not correspond to the MsbA dimer in vivo. An alternative model of the dimer is discussed in the context of available experimental data.

ATP-Binding Cassette Transporters↗

PubMed2003

Mechanosensitive channels: stress relief.

Bacterial responses to decreasing osmolality involve mechanosensitive channels. The crystal structure has been determined of the small conductance mechanosensitive channel (MscS) from Escherichia coli, providing new insights into mechanical and voltage sensing by this and other channel proteins.

Escherichia coli↗

PubMed2002

Potassium channels: structures, models, simulations.

Potassium channels have been studied intensively in terms of the relationship between molecular structure and physiological function. They provide an opportunity to integrate structural and computational studies in order to arrive at an atomic resolution description of mechanism. We review recent progress in K channel structural studies, focussing on the bacterial channel KcsA. Structural studies can be extended via use of computational (i.e. molecular simulation) approaches in order to provide a perspective on aspects of channel function such as permeation, selectivity, block and gating. Results from molecular dynamics simulations are shown to be in good agreement with recent structural studies of KcsA in terms of the interactions of K(+) ions with binding sites within the selectivity filter of the channel, and in revealing the importance of filter flexibility in channel function. We discuss how the KcsA structure may be used as a template for developing structural models of other families of K channels. Progress in this area is explored via two examples: inward rectifier (Kir) and voltage-gated (Kv) potassium channels. A brief account of structural studies of ancillary domains and subunits of K channels is provided.

Amino Acid Sequence↗

PubMed2002

Glutamate receptors: desensitizing dimers.

Recent structural studies show, not only how the desensitization of a ligand-gated ion channel with bound agonist can be rationalized in terms of subunit-subunit instability, but also how a previously unknown mode of interaction may provide clues into how the receptor is tetramerically assembled in vivo.

Animals↗

PubMed2002

Open-state models of a potassium channel.

The structure of the bacterial potassium channel, KcsA, corresponds to the channel in a closed state. Two lines of evidence suggest that the channel must widen its intracellular mouth when in an open state: 1) internal block by a series of tetraalkylammonium ions and 2) spin labeling experiments. Thus it is known that the protein moves in this region, but it is unclear by how much and the mechanisms that are involved. To address this issue we have applied a novel approach to generate plausible open-state models of KcsA. The approach can be thought of as placing a balloon inside the channel and gradually inflating it. Only the protein sees the balloon, and so water is free to move in and out of the channel. The balloon is a van der Waals sphere whose parameters change by a small amount at each time step, an approach similar to methods used in free energy perturbation calculations. We show that positioning of this balloon at various positions along the pore axis generates similar open-state models, thus indicating that there may be a preferred pathway to an open state. We also show that the resulting structures from this process are conformationally unstable and need to undergo a relaxation process for up to 4 ns. We show that the channel can relax into a new state that has a larger pore radius at the region of the intracellular mouth. The resulting models may be useful in exploring models of the channel in the context of ion permeation and blocking agents.

Bacterial Proteins↗

PubMed2002

K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study.

Molecular dynamics simulations of a bacterial potassium channel (KcsA) embedded in a phospholipid bilayer reveal significant differences in interactions of the selectivity filter with K(+) compared with Na(+) ions. K(+) ions and water molecules within the filter undergo concerted single-file motion in which they translocate between adjacent sites within the filter on a nanosecond timescale. In contrast, Na(+) ions remain bound to sites within the filter and do not exhibit translocation on a nanosecond timescale. Furthermore, entry of a K(+) ion into the filter from the extracellular mouth is observed, whereas this does not occur for a Na(+) ion. Whereas K(+) ions prefer to sit within a cage of eight oxygen atoms of the filter, Na(+) ions prefer to interact with a ring of four oxygen atoms plus two water molecules. These differences in interactions in the selectivity filter may contribute to the selectivity of KcsA for K(+) ions (in addition to the differences in dehydration energy between K(+) and Na(+)) and the block of KcsA by internal Na(+) ions. In our simulations the selectivity filter exhibits significant flexibility in response to changes in ion/protein interactions, with a somewhat greater distortion induced by Na(+) than by K(+) ions.

Biophysical Phenomena↗

PubMed2002

Molecular dynamics simulations of the ligand-binding domain of the ionotropic glutamate receptor GluR2.

Ionotropic glutamate receptors are essential for fast synaptic nerve transmission. Recent x-ray structures for the ligand-binding (S1S2) region of the GluR2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-sensitive receptor have suggested how differences in protein/ligand interactions may determine whether a ligand will behave as a full agonist. We have used multiple molecular dynamics simulations of 2-5 ns duration to explore the structural dynamics of GluR2 S1S2 in the presence and absence of glutamate and in a complex with kainate. Our studies indicate that not only is the degree of domain closure dependent upon interactions with the ligand, but also that protein/ligand interactions influence the motion of the S2 domain with respect to S1. Differences in domain mobility between the three states (apo-S1S2, glutamate-bound, and kainate-bound) are surprisingly clear-cut. We discuss how these changes in dynamics may provide an explanation relating the mechanism of transmission of the agonist-binding event to channel opening. We also show here how the glutamate may adopt an alternative mode of binding not seen in the x-ray structure, which involves a key threonine (T480) side chain flipping into a new conformation. This new conformation results in an altered pattern of hydrogen bonding at the agonist-binding site.

Algorithms↗

PubMed2002

Water in ion channels and pores--simulation studies.

The microscopic properties of water in narrow pores are relevant to the function of ion channels and related membrane transport proteins. The emergence of several high-resolution structures allows one to perform molecular dynamics simulation studies of water in such pores. Simulations of bundles of parallel alpha-helical peptides (e.g. alamethicin) have enabled development of methodologies and concepts appropriate to such investigations. In the narrow channels formed by such bundles, water molecules exhibit reduced rotational and translation motion. This reduction in water mobility may be a general property of narrow pores. We have used simplified channel models to explore the role of hydrophobicity/hydrophilicity in the entry of water into pores. Narrow pores with a hydrophobic lining, although physically open, may not admit water molecules, acting as a 'hydrophobic gate' that prevents water and ion permeation. Such a gate can be opened either by widening the pore or making its lining more polar. Simulations have been used to explore the behaviour of water in GlpF, a member of the aquaporin family of water pores, and OmpA, a bacterial outer membrane protein. Preliminary results suggest that a continuous water wire is not formed within the amphipathic GlpF pore. Simulations of OmpA, in which polar residues line the channel, indicate that a small conformational change in one of the channel lining side chains may open the channel. In summary, comparison of the behaviour of water in different narrow transmembrane pores suggests that an amphipathic pore is ideal for water permeation, and that either a highly hydrophobic pore lining or a charged pore-lining region can act as a gate.

Computer Simulation↗