Xiaojing Ma

Beta structure motifs of islet amyloid polypeptides identified through surface-mediated assemblies

We report here the identification of the key sites for the beta structure motifs of the islet amyloid polypeptide (IAPP) analogs by using scanning tunneling microscopy (STM). Duplex folding structures in human IAPP8–37 (hIAPP8–37) assembly were observed featuring a hairpin structure. The multiplicity in rIAPP assembly structures indicates the polydispersity of the rat IAPP8–37 (rIAPP8–37) beta-like motifs. The bimodal length distribution of beta structure motifs for rIAPP8–37 R18H indicates the multiple beta segments linked by turns. The IAPP8–37 analogs share common structure motifs of IAPP8–17 and IAPP26–37 with the most probable key sites at positions around Ser19/Ser20 and Gly24. These observations reveal the similar amyloid formation tendency in the C and N terminus segments because of the sequence similarity, while the differences in specific amino acids at each key site manifest the effect of sequence variations. The results could be beneficial for studying structural polymorphism of amyloidal peptides with multiple beta structure motifs.

Amyloid β (1–42) Folding Multiplicity and Single-Molecule Binding Behavior Studied with STM

The fine folding and assembling characteristics of amyloid beta (Abeta) peptides are important to pharmaceutical studies of drug molecules and to the pathological analysis of neurodegenerative disorders such as Alzheimers disease at the molecular level. Here we present observations of the multiple folding characteristics of amyloid peptide Abeta(42) lamellae using scanning tunneling microscopy. Molecularly resolved core regions of Abeta(42) hairpins and unfolded peptide assembly structures are identified. The parallel assembling characteristics of Abeta(42) hairpins can be confirmed in the study. In addition, single-molecule binding characteristics of Congo red and thioflavin T have been shown to bind at the groove regions of peptide assemblies. This study demonstrates a complementary venue for studying molecular heterogeneity of peptide assemblies, as well as the binding characteristics of molecular modulators.

Sequence effects on peptide assembly characteristics observed by using scanning tunneling microscopy

Homogeneous assemblies of the model peptides at interfaces have been achieved and observed with scanning tunneling microscopy. The dependence of the observed brightness in STM images is analyzed, and the correlation with the peptide residues is proposed. We have also investigated the conformational dynamics of the peptide assemblies adsorbed on a graphene sheet by performing all-atom molecular dynamic simulations in water at 300 K. The simulation results of the two peptide assemblies on graphite surfaces show that R(4)G(4)H(8) and F(4)G(4)H(8) peptide assemblies are mostly in β-sheet structure, and the interaction energy of the four different residues with graphite surfaces follows the order of Phe > His > Arg > Gly, consistent with their brightness contrasts in STM images. The insight on the distribution of residue moieties in the peptide assemblies could provide beneficial venues for studying peptide-based interfacial processes such as site-specific interactions between molecular species with peptides.

Structural characteristics of the beta-sheet-like human and rat islet amyloid polypeptides as determined by scanning tunneling microscopy

We demonstrate in this work that scanning tunneling microscopy (STM) provides a useful approach to obtaining structural information about human islet amyloid polypeptide (hIAPP) and rat islet amyloid polypeptide (rIAPP) assembly on highly oriented pyrolytic graphite (HOPG) with sub-molecular resolution. The observed hIAPP and rIAPP lamellae consisted of parallel stripes. The STM images of hIAPPs show multiple molecular folding structures, with an average of 11 amino acid residues for the core regions. In addition, the STM images also reveal the assembly characteristics of rIAPP lamellae and may indicate a secondary structural conformation from random coil to beta-sheet-like on the graphite surface.

NHS-ester functionalized poly(PEGMA) brushes on silicon surface for covalent protein immobilization.

Poly(PEGMA) homopolymer brushes were developed by atom transfer radical polymerization (ATRP) on the initiator-modified silicon surface (Si-initiator). Through covalent binding, protein immobilization on the poly(PEGMA) films was enabled by further NHS-ester functionalization of the poly(PEGMA) chain ends. The formation of polymer brushes was confirmed by assessing the surface composition (XPS) and morphology (atomic force microscopy (AFM), scanning electronic microscopy (SEM)) of the modified silicon wafer. The binding performance of the NHS-ester functionalized surfaces with two proteins horseradish peroxidase (HRP) and chicken immunoglobulin (IgG) was monitored by direct observation. These results suggest that this method which incorporates the properties of polymer brush onto the binding surfaces may be a good strategy suitable for covalent protein immobilization.

Binding modes of thioflavin T molecules to prion peptide assemblies identified by using scanning tunneling microscopy.

The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches.

Molecular miscibility characteristics of self-assembled 2D molecular architectures

Various molecular networks, stabilized by hydrogen bonds or van der Waals interactions, are demonstrated in which the distribution of heterogeneous molecular species could be controlled at the level of single molecules or molecular clusters. The observed miscibility characteristics of the two-dimensional (2D) assembly structures could enable studies on the heterogeneous molecular interfaces of guest–host architectures. In addition, it could be envisioned that large cavity networks should be beneficial for studying the clustering behavior of molecular aggregates of similar or dissimilar species, chemical interactions in nanometre scale constrained areas, as well as the design of complex molecular architectures.

Molecular level studies on binding modes of labeling molecules with polyalanine peptides

In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(II) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO(3)Na)(4))) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO(3)Na)(4) display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.

Two-dimensional rigid molecular network with elastic boundaries for constructing hybrid molecular assemblies

The star-shaped molecule, 2,6,10-trihexyloxy-3,7,11-tris[3,4,5-tris(dodecyloxy)benzoyloxy]triphenylene (sym) was used as the building unit for constructing porous molecular networks with large cavities. It has been identified that a variety of guest molecules (such as C60, phthalocyanine and substituted phthalocyanine) can be dispersed in this template to form supramolecular architectures, which were also studied by scanning tunneling microscopy (STM). It is interesting to observe that this template has elastic boundaries and rigid structures, which can accommodate different amounts of guest species by interacting with them, while keeping the size of cavities invariable.

ELECTRIC-FIELD DEPENDENCE OF MOLECULAR CONFORMATIONS OBSERVED BY USING SCANNING TUNNELING MICROSCOPY

We review the progress in observation of electrically induced conformational changes of a range of single molecules and molecular assemblies using scanning tunneling microscopy (STM). Recent results using species with optical active functional groups and supramolecular structures confirmed the previously observed effects that the cholesterol molecules with soft linkers have the conformational bistability when switching the bias polarity, while no discernable changes were observed for the mesogen molecules, containing rigid linking units. In addition, it was also observed that the linker units could have appreciable impacts on the assembling characteristics.