Observation of glycine zipper and unanticipated occurrence of ambidextrous helices in the crystal structure of a chiral undecapeptide

<p>Abstract</p> <p>Background</p> <p>The <it>de novo </it>design of peptides and proteins has recently surfaced as an approach for investigating protein structure and function. This approach vitally tests our knowledge of protein folding and function, while also laying the groundwork for the fabrication of proteins with properties not precedented in nature. The success of these studies relies heavily on the ability to design relatively short peptides that can espouse stable secondary structures. To this end, substitution with α, β-dehydroamino acids, especially α, β-dehydrophenylalanine (ΔPhe) comes in use for spawning well-defined structural motifs. Introduction of ΔPhe induces β-bends in small and 3₁₀-helices in longer peptide sequences.</p> <p>Results</p> <p>The present report is an investigation of the effect of incorporating two glycines in the middle of a ΔPhe containing undecapeptide. A de novo designed undecapeptide, Ac-Gly¹-Ala²-ΔPhe³-Leu⁴-Gly⁵-ΔPhe⁶-Leu⁷-Gly⁸-ΔPhe⁹-Ala¹⁰-Gly¹¹-NH₂, was synthesized and characterized using X-ray diffraction and Circular Dichroism spectroscopic methods. Crystallographic studies suggest that, despite the presence of L-amino acid (L-Ala and L-Leu) residues in the middle of the sequence, the peptide adopts a 3₁₀-helical conformation of ambidextrous screw sense, one of them a left-handed (A) and the other a right-handed (B) 3₁₀-helix with A and B being antiparallel to each other. However, CD studies reveal that the undecapeptide exclusively adopts a right-handed 3₁₀-helical conformation. In the crystal packing, three different interhelical interfaces, Leu-Leu, Gly-Gly and ΔPhe-ΔPhe are observed between the helices A and B. A network of C-H...O hydrogen bonds are observed at ΔPhe-ΔPhe and Gly-Gly interhelical interfaces. An important feature observed is the occurrence of glycine zipper motif at Gly-Gly interface. At this interface, the geometric pattern of interhelical interactions seems to resemble those observed between helices in transmembrane (TM) proteins.</p> <p>Conclusion</p> <p>The present design strategy can thus be exploited in future work on de novo design of helical bundles of higher order and compaction utilizing ΔPhe residues along with GXXG motif.</p

De novo design of a transmembrane Zn²⁺-transporting four-helix bundle.

The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn(2+) and Co(2+), but not Ca(2+), across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn(2+) ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties

Computational Design of a Protein Crystal

Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a “honeycomb-like” structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify “designable” structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis

Protein-Directed Self-Assembly of a Fullerene Crystal

Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C 60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C 60 in solution, rendering it water soluble. Two tetramers associate with one C 60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers. Strikingly, the assembly exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C 60 are electrically insulating. The affinity of C 60 for its crystal-binding site is estimated to be in the nanomolar range, with lattices of known protein crystals geometrically compatible with incorporating the motif. Taken together, these findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design

Dehydrophenylalanine (\Delta Phe) as a \beta Breaker:Extended Structure Terminated by a \Delta Phe-Induced Turn in the Pentapeptide Boc-Phe1-Ala2-Ile3-\Delta Phe4-Ala5-OMe

Amyloid is a highly insoluble, aggregated state of certain polypeptide sequences associated with a range of debilitating diseases.A key step in amyloid formation is the transition of a protein from its native structure to a \beta-sheet arrangement; this suggests that the prevention of the ability of amyloidogenic proteins to adopt a \beta-sheet conformation would be useful as a way to impede the amyloid self-assembly process[1].The use of \beta-breaker residues is one approach for the development of peptide-based fibrillization-inhibiting drugs. Soto et al. demonstrated that the incorporation of \beta-sheet-breaker elements into short peptides composed of the recognition sequence of the amyloidogenic proteins inhibited amyloid formation. In this context, \beta-sheet-breaker residues, such as proline and a-aminoisobutyric acid (Aib), which is an unnatural amino acid residue, have been found to inhibit amyloid fibril formation.$^{[2a-d]}

The Population Development of Latin America in 1950 - 2005

<p><b>Copyright information:</b></p><p>Taken from "Observation of glycine zipper and unanticipated occurrence of ambidextrous helices in the crystal structure of a chiral undecapeptide"</p><p>http://www.biomedcentral.com/1472-6807/7/51</p><p>BMC Structural Biology 2007;7():51-51.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2042501.</p><p></p

Chloroform-methanol titration depicting maximum intensity at 50: 50 CHCl: MeOH

<p><b>Copyright information:</b></p><p>Taken from "Observation of glycine zipper and unanticipated occurrence of ambidextrous helices in the crystal structure of a chiral undecapeptide"</p><p>http://www.biomedcentral.com/1472-6807/7/51</p><p>BMC Structural Biology 2007;7():51-51.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2042501.</p><p></p