Internal actin filament dynamics in the presence of vinculin: a dynamic light scattering study

Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data

Background

Over the past decade our laboratory has focused on understanding how soluble cytoskeleton-associated proteins interact with membranes and other lipid aggregates. Many protein domains mediating specific cell membrane interactions appear by fluorescence microscopy and other precision techniques to be partially inserted into the lipid bilayer. It is unclear whether these protein-lipid-interactions are dependent on shared protein motifs or unique regional physiochemistry, or are due to more global characteristics of the protein.

Results

We have developed a novel computational program that predicts a protein's lipid-binding site(s) from primary sequence data. Hydrophobic labeling, Fourier transform infrared spectroscopy (FTIR), film balance, T-jump, CD spectroscopy and calorimetry experiments confirm that the interfaces predicted for several key cytoskeletal proteins (alpha-actinin, Arp2, CapZ, talin and vinculin) partially insert into lipid aggregates. The validity of these predictions is supported by an analysis of the available three-dimensional structural data. The lipid interfaces predicted by our algorithm generally contain energetically favorable secondary structures (e.g., an amphipathic alpha-helix flanked by a flexible hinge or loop region), are solvent-exposed in the intact protein, and possess favorable local or global electrostatic properties.

Conclusion

At present, there are few reliable methods to determine the region of a protein that mediates biologically important interactions with lipids or lipid aggregates. Our matrix-based algorithm predicts lipid interaction sites that are consistent with the available biochemical and structural data. To determine whether these sites are indeed correctly identified, and whether use of the algorithm can be safely extended to other classes of proteins, will require further mapping of these sites, including genetic manipulation and/or targeted crystallography.

Structure and dynamics in solvent-polarity-induced aggregates from a c60 fullerene-based dyad

A novel methanofullerene dyad based on a hydrophobic (acceptor C60 moiety)-hydrophilic (bridge with benzene and ester functionalities)-hydrophobic (donor didodecyloxybenzene) network is designed and synthesized. Electronic absorption spectral features revealed the molecule to exhibit a strong tendency to self-aggregate in binary solvent mixtures at room temperature, where the dielectric constant exceeds a critical value, approximately 30. The dynamic structure factors of these spherical aggregates revealed stretched exponential decay with sizes varying between 110 and 250 nm with an increasing concentration, estimated from the dynamic light scattering experiments. However, a loss of shape selectivity of these aggregates was noted at lower water volume fractions in the binary solvent mixtures. The water-extracted spherical clusters were identified to be fractals with a dimension of 1.85, leading to diffusion-limited cluster aggregation as the mechanistic route for clusterization.

Binding of tropomyosin-troponin to actin increases filament bending stiffness

Rheologic measurements show that the association of tropomyosin-troponin with actin filaments is responsible for the reduction of the internal chain dynamic and increase in the mechanical rigidity of actin filaments. Basing calculations on the linear relation between the plateau modulus, G(N)('), and bending modulus, kappa, I find that tropomyosin-troponin at r(AT) = 7 increases actin filament stiffness by approximately 50%. This is confirmed by dynamic light scattering. Further increases are observed at rising F-actin and constant tropomyosin-troponin concentrations. Tropomyosin-troponin also delays actin assembly and subsequent network formation and increases filament stiffness over time.

Mg- and Ca-actin filaments appear virtually identical in steady-state as determined by dynamic light scattering

Dynamic light scattering measurements show that although Mg-actin polymerizes more rapidly than Ca-actin (actin at 0.04-0.4 mg/ml polymerized with 0.1 M KCl +/- 2 mM MgCl2 or CaCl2, at room temperature or at 10 degrees C), steady-state filaments exhibit nearly identical intensity autocorrelation functions and similar mean scattered intensities. The dynamic data are used to measure the persistence length of the filaments which is found to be 4.2 microns independent of the bound cation and of the actin concentration.

Interaction of the 47-kDa talin fragment and the 32-kDa vinculin fragment with acidic phospholipids: a computer analysis

In recent in vitro experiments, it has been demonstrated that the 47-kDa fragment of the talin molecule and the 32-kDa fragment of the vinculin molecule interact with acidic phospholipids. By using a computer analysis method, we determined the hydrophobic and amphipathic stretches of these fragments and, by applying a purpose-written matrix method, we ascertained the molecular amphipathic structure of alpha-helices. Calculations for the 47-kDa mouse talin fragment (residues 1-433; NH2-terminal region) suggest specific interactions of residues 21-39, 287-342, and 385-406 with acidic phospholipids and a general lipid-binding domain for mouse talin (primary amino acid sequence 385-401) and for Dictyostelium talin (primary amino acid sequence 348-364). Calculations for the 32-kDa chicken embryo vinculin fragment (residues 858-1066; COOH-terminal region) and from nematode vinculin alignment indicate for chicken embryo vinculin residues 935-978 and 1020-1040 interactions with acidic phospholipids. Experimental confirmation has been given for vinculin (residues 916-970), and future detailed experimental analyses are now needed to support the remaining computational data.