Molecular modeling studies on CNG channel from bovine retinal rod: a structural model of the cyclic nucleotide-binding domain

In silico description of fluorescent probes in vivo

Fluorescent imaging in vivo has became one of the most powerful tools to follow the temporal and spatial localization of a variety of intracellular molecular events. Genetically encoded fluorescent indicators using the FRET effect are routinely used although the molecular basis regulating their functioning is not completely known. Here, the structural and dynamics properties of a commonly used FRET sensor for the second messenger cAMP based on the cAMP-binding domains of the regulatory subunit of Protein Kinase A are presented. Molecular dynamics simulations allowed pinpointing the main features of cAMP driven conformational transition and dissecting the contributions of geometric factors governing the functioning of the biosensor. Simulations suggest that, although orientational factors are not fully isotropic, they are highly dynamic making the inter-chromophore distance the dominant feature, determining the functioning of the probes. It is expected that this computer-aided methodology may state general basis for rational design strategies of fluorescent markers for in vivo imaging.

Catabolite Activator Protein in Aqueous Solution: A Molecular Simulation Study

The homodimeric catabolite activator protein (CAP) is a bacterial DNA binding transcription regulator whose activity is controlled by the binding of the intracellular mediator cyclic adenosine monophosphate (cAMP). Each CAP subunit consists of a cyclic nucleotide and a DNA binding domain. Here, we investigate the structural features of the ligand-bound CAP in aqueous solution by molecular dynamics simulations based on the available X-ray structures (Passner et al. J. Mol. Biol. 2000, 304, 847-859 and Chen et al. J. Mol. Biol. 2001, 314, 63-74). Our calculations suggest that the homodimer in solution assumes a symmetric arrangement in which both DNA binding domains are separated from the respective cyclic nucleotide binding domains by a cleft. This contrasts with the X-ray structure, which exhibits instead an asymmetric conformation. On the basis of electrostatics calculations, we propose that the symmetric structure in solution may be an important feature for DNA molecular recognition.

cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations

The hyperpolarization-activated cyclic nucleotide-modulated (HCN) cation channels are opened by membrane hyperpolarization, while their activation is modulated by the binding of cyclic adenosine monophosphate (cAMP) in the cytoplasm. Here we investigate the molecular basis of cAMP channel modulation by performing molecular dynamics simulations of a segment comprising the C-linker and the cyclic nucleotide binding domain (CNBD) in the presence and absence of cAMP, based on the available crystal structure of HCN2 from mouse. In presence of cAMP, the protein undergoes an oscillation of the quaternary structure on the order of 10 ns, not observed in the apoprotein. In contrast, the absence of ligand causes conformational rearrangements within the CNBDs, driving these domains to a more flexible state, similar to that described in CNBDs of other proteins. This increased flexibility causes a rather disordered movement of the CNBDs, resulting in an inhibitory effect on the channel. We propose that the cAMP-triggered large-scale oscillation plays an important role for the channel's function, being coupled to a motion of the C-linker which, in turn, modulates the gating of the channel.

PKA-dependent and PKA-independent pathways for cAMP-regulated exocytosis

Stimulus-secretion coupling is an essential process in secretory cells in which regulated exocytosis occurs, including neuronal, neuroendocrine, endocrine, and exocrine cells. While an increase in intracellular Ca(2+) concentration ([Ca(2+)](i)) is the principal signal, other intracellular signals also are important in regulated exocytosis. In particular, the cAMP signaling system is well known to regulate and modulate exocytosis in a variety of secretory cells. Until recently, it was generally thought that the effects of cAMP in regulated exocytosis are mediated by activation of cAMP-dependent protein kinase (PKA), a major cAMP target, followed by phosphorylation of the relevant proteins. Although the involvement of PKA-independent mechanisms has been suggested in cAMP-regulated exocytosis by pharmacological approaches, the molecular mechanisms are unknown. Newly discovered cAMP-GEF/Epac, which belongs to the cAMP-binding protein family, exhibits guanine nucleotide exchange factor activities and exerts diverse effects on cellular functions including hormone/transmitter secretion, cell adhesion, and intracellular Ca(2+) mobilization. cAMP-GEF/Epac mediates the PKA-independent effects on cAMP-regulated exocytosis. Thus cAMP regulates and modulates exocytosis by coordinating both PKA-dependent and PKA-independent mechanisms. Localization of cAMP within intracellular compartments (cAMP compartmentation or compartmentalization) may be a key mechanism underlying the distinct effects of cAMP in different domains of the cell.

Molecular basis of the allosteric mechanism of cAMP in the regulatory PKA subunit

The second messenger cyclic Adenosine MonoPosphate (cAMP) mediates many biological process by interacting with structurally conserved nucleotide binding domains (cNBD's). Here, we use molecular dynamics simulations on RIIbeta-PKA, one of the best characterized members of the cNBD family, in presence and absence of cAMP. The results of our calculations are fully consistent with the available experimental data and suggest that the key factor of the cAMP allosteric mechanism in cNBDS's is the increased flexibility of the protein upon ligand release along with a mechanical coupling between helical segments. In addition, our calculations provide a rationale for the experimentally observed cAMP selective binding to PKA.

Molecular modeling of ion channels: structural predictions

Recent advances in membrane protein crystallography have greatly increased structural information of channels permeating metal ions. Structural bioinformatics techniques and molecular dynamics calculations are providing structural models of ion channels for which the three-dimensional structure is not known. Most of the reported structure prediction studies focus on K(+) channels and are based on the KcsA K(+) channel structure.