Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein.

Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.

Control of Protein Conformation and Orientation on Graphene.

Graphene-based biosensors have attracted considerable attention due to their advantages of label-free detection and high sensitivity. Many such biosensors utilize noncovalent van der Waals force to attach proteins onto graphene surface while preserving graphene's high conductivity. Maintaining the protein structure without denaturation/substantial conformational change and controlling proper protein orientation on the graphene surface are critical for biosensing applications of these biosensors fabricated with proteins on graphene. Based on the knowledge we obtained from our previous experimental study and computer modeling of amino acid residual level interactions between graphene and peptides, here we systemically redesigned an important protein for better conformational stability and desirable orientation on graphene. In this paper, immunoglobulin G (IgG) antibody-binding domain of protein G (protein GB1) was studied to demonstrate how we can preserve the protein native structure and control the protein orientation on graphene surface by redesigning protein mutants. Various experimental tools including sum frequency generation vibrational spectroscopy, attenuated total refection-Fourier transform infrared spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy were used to study the protein GB1 structure on graphene, supplemented by molecular dynamics simulations. By carefully designing the protein GB1 mutant, we can avoid strong unfavorable interactions between protein and graphene to preserve protein conformation and to enable the protein to adopt a preferred orientation. The methodology developed in this study is general and can be applied to study different proteins on graphene and beyond. With the knowledge obtained from this research, one could apply this method to optimize protein function on surfaces (e.g., to enhance biosensor sensitivity).

Investigating the Effect of Two-Point Surface Attachment on Enzyme Stability and Activity.

Immobilization on solid supports provides an effective way to improve enzyme stability and simplify downstream processing for biotechnological applications, which has been widely used in research and in applications. However, surface immobilization may disrupt enzyme structure due to interactions between the enzyme and the supporting substrate, leading to a loss of the enzyme catalytic efficiency and stability. Here, we use a model enzyme, nitroreductase (NfsB), to demonstrate that engineered variants with two strategically positioned surface-tethering sites exhibit improved enzyme stability when covalently immobilized onto a surface. Tethering sites were designed based on molecular dynamics (MD) simulations, and enzyme variants containing cysteinyl residues at these positions were expressed, purified, and immobilized on maleimide-terminated self-assembled monolayer (SAM) surfaces. Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy were used to deduce the NfsB enzyme orientations, which were found to be consistent with those predicted from the MD simulations. Thermal stability analyses demonstrated that NfsB variants immobilized through two tethering sites exhibited generally improved thermal stability compared with enzymes tethered at only one position. For example, NfsB enzyme chemically immobilized via positions 423 and 111 exhibits at least 60% stability increase compared to chemically immobilized NfsB mutant via a single site. This research develops a generally applicable and systematic approach using a combination of simulation and experimental methods to rationally select protein immobilization sites for the optimization of surface-immobilized enzyme activity and stability.

Simultaneous Observation of the Orientation and Activity of Surface-Immobilized Enzymes.

Surface immobilized enzymes have been widely used in many applications such as biosensors, biochips, biofuel production, and biofuel cell construction. Many factors dictate how enzymes' structure, activity, and stability may change when immobilized, including surface functionalization, immobilization chemistry, nature of the solid support, and enzyme surface density. To better understand how immobilization affects enzyme structure and activity, we have developed a method to measure both surface-sensitive protein vibrational spectra and enzymatic activity simultaneously. To accomplish this, an optical/fluorescence microscope was incorporated into a sum frequency generation (SFG) spectrometer. Using ß-glucosidase (ß-Glu) as a model system, enzymes were covalently tethered to a self-assembled monolayer surface using cysteine-maleimide chemistry. Their orientations were determined by SFG spectroscopy, with a single native cysteine residue oriented toward the functionalized surface, and activity measured simultaneously using a fluorogenic substrate resorufin ß-d-glucopyranoside, with a loss of activity of 53% as compared to comparable solution measurements. Measuring ß-Glu activity and orientation simultaneously provides more accurate information for designing and further improving enzymatic activity of surface-bound enzymes.

Engineered Surface-Immobilized Enzyme that Retains High Levels of Catalytic Activity in Air.

In the absence of aqueous buffer, most enzymes retain little or no activity; however, "water-free" enzymes would have many diverse applications. Here, we describe the chemically precise immobilization of an enzyme on an engineered surface designed to support catalytic activity in air at ambient humidity. Covalent immobilization of haloalkane dehalogenase on a surface support displaying poly(sorbitol methacrylate) chains resulted in ∼40-fold increase in activity over lyophilized enzyme powders for the gas-phase dehalogenation of 1-bromopropane. The activity of the immobilized enzyme in air approaches 25% of the activity obtained in buffer for the immobilized enzyme. Poly(sorbitol methacrylate) appears to enhance activity by replacing protein-water interactions, thereby preserving the protein structure.

Molecular Interactions between Graphene and Biological Molecules.

Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e.g., to detect analytes in solution). To control and characterize peptide behavior on a graphene surface in solution is difficult. Here we successfully probed the molecular interactions between two peptides (cecropin P1 and MSI-78(C1)) and graphene in situ and in real-time using sum frequency generation (SFG) vibrational spectroscopy and molecular dynamics (MD) simulation. We demonstrated that the distribution of various planar (including aromatic (Phe, Trp, Tyr, and His)/amide (Asn and Gln)/Guanidine (Arg)) side-chains and charged hydrophilic (such as Lys) side-chains in a peptide sequence determines the orientation of the peptide adsorbed on a graphene surface. It was found that peptide interactions with graphene depend on the competition between both planar and hydrophilic residues in the peptide. Our results indicated that part of cecropin P1 stands up on graphene due to an unbalanced distribution of planar and hydrophilic residues, whereas MSI-78(C1) lies down on graphene due to an even distribution of Phe residues and hydrophilic residues. With such knowledge, we could rationally design peptides with desired residues to manipulate peptide-graphene interactions, which allows peptides to adopt optimized structure and exhibit excellent activity for nanobio-technological applications. This research again demonstrates the power to combine SFG vibrational spectroscopy and MD simulation in studying interfacial biological molecules.

Image restoration based on phase conjugation in second-order nonlinear materials under reflection configuration.

We have demonstrated the recovery of the distorted images by a phase plate to nearly their original qualities under a refection configuration. This is made possible by utilizing difference-frequency generation in a bulk KTiOPO(4) (KTP) crystal and an AFB-KTP crystal composite. In such a geometry, both input and phase-conjugated waves propagate through the distorted phase plate for a round trip. They are reflected by the object, which can be far away from the imaging system, and captured by the cameras. Therefore, such a configuration is much more practical for eventually deploying our imaging system for realizing practical applications. We have demonstrated the advantages of the imaging system such as polarization insensitivity and broadband capability.

Terahertz conductivity of topological surface states in Bi1.5Sb0.5Te1.8Se1.2.

Topological insulators are electronic materials with an insulating bulk and conducting surface. However, due to free carriers in the bulk, the properties of the metallic surface are difficult to detect and characterize in most topological insulator materials. Recently, a new topological insulator Bi1.5Sb0.5Te1.7Se1.3 (BSTS) was found, showing high bulk resistivities of 1-10 Ω.cm and greater contrast between the bulk and surface resistivities compared to other Bi-based topological insulators. Using Terahertz Time-Domain Spectroscopy (THz-TDS), we present complex conductivity of BSTS single crystals, disentangling the surface and bulk contributions. We find that the Drude spectral weight is 1-2 orders of magnitude smaller than in other Bi-based topological insulators, and similar to that of Bi2Se3 thin films, suggesting a significant contribution of the topological surface states to the conductivity of the BSTS sample. Moreover, an impurity band is present about 30 meV below the Fermi level, and the surface and bulk carrier densities agree with those obtained from transport data. Furthermore, from the surface Drude contribution, we obtain a ~98% transmission through one surface layer--this is consistent with the transmission through single-layer or bilayer graphene, which shares a common Dirac-cone feature in the band structure.

Restoration of blurred images due to phase distortion based on polarization-insensitive phase conjugation in second-order nonlinear medium.

Broadband and polarization-insensitive phase conjugation, achieved based on difference-frequency generation in a second-order nonlinear composite consisting of stacked KTiOPO(4) (KTP) plates, was exploited to restore blurred images due to phase distortion as a novel scheme. Due to the quasi-phase matching in the stacked KTP crystals, our result reveals that the image restoration is insensitive to the polarization direction and wavelength of the input beam.

Terahertz conductivity of twisted bilayer graphene.

Using terahertz time-domain spectroscopy, the real part of optical conductivity [σ(1)(ω)] of twisted bilayer graphene was obtained at different temperatures (10-300 K) in the frequency range 0.3-3 THz. On top of a Drude-like response, we see a strong peak in σ(1)(ω) at ~2.7 THz. We analyze the overall Drude-like response using a disorder-dependent (unitary scattering) model, then attribute the peak at 2.7 THz to an enhanced density of states at that energy, which is caused by the presence of a van Hove singularity arising from a commensurate twisting of the two graphene layers.