Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.

Large scale epitaxial growth and transfer of monolayer MoS has attracted great attention in recent years. Here, we report the wafer-scale epitaxial growth of highly oriented continuous and uniform monolayer MoS films on single-crystalline sapphire wafers by chemical vapor deposition (CVD) method. The epitaxial film is of high quality and stitched by many 0°, 60° domains and 60°-domain boundaries. Moreover, such wafer-scale monolayer MoS films can be transferred and stacked by a simple stamp-transfer process, and the substrate is reusable for subsequent growth. Our progress would facilitate the scalable fabrication of various electronic, valleytronic, and optoelectronic devices for practical applications.

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The recent discovery of ferromagnetism in two-dimensional (2D) van der Waals (vdW) materials holds promises for spintronic devices with exceptional properties. However, to use 2D vdW magnets for building spintronic nanodevices such as magnetic memories, key challenges remain in terms of effectively switching the magnetization from one state to the other electrically. Here, we devise a bilayer structure of Fe3GeTe2/Pt, in which the magnetization of few-layered Fe3GeTe2 can be effectively switched by the spin-orbit torques (SOTs) originated from the current flowing in the Pt layer. The effective magnetic fields corresponding to the SOTs are further quantitatively characterized using harmonic measurements. Our demonstration of the SOT-driven magnetization switching in a 2D vdW magnet could pave the way for implementing low-dimensional materials in the next-generation spintronic applications.

Two-dimensional molybdenum disulfide (MoS 2 ) is an emergent semiconductor with great potential in next-generation scaled-up electronics, but the production of high-quality monolayer MoS 2 wafers still remains a challenge. Here, we report an epitaxy route toward 4 in. monolayer MoS 2 wafers with highly oriented and large domains on sapphire. Benefiting from a multisource design for our chemical vapor deposition setup and the optimization of the growth process, we successfully realized material uniformity across the entire 4 in. wafer and greater than 100 μm domain size on average. These monolayers exhibit the best electronic quality ever reported, as evidenced from our spectroscopic and transport characterizations. Our work moves a step closer to practical applications of monolayer MoS 2 .

A peptide construct (FPtr) was synthesized which mimics the biologically relevant topology of fusion peptide (FP) domains of the trimeric HIV-1 gp41 envelope protein. The FP domains play a critical role in gp41-catalyzed fusion of viral and host cell membranes which is a key step in viral infection. The FPtr construct contains three FP strands chemically bonded at their C-termini through lysine side chains. Analytical ultracentrifugation demonstrated that FPtr does not self-associate in aqueous solution and therefore models the expected FP topology of gp41. Comparative functional fusion assays were carried out using FPtr, FPdm (a cross-linked FP dimer construct), and FPmn (FP monomer). The derived fusion rate constants order ktr > kdm > kmn, and the ratio ktr/kmn has values in the range of 15-40. These results suggest that there is strong correlation of the fusion rate with the biologically relevant trimeric FP topology.

The human immunodeficiency virus (HIV) fusion peptide (HFP) is the N-terminal apolar region of the HIV gp41 fusion protein and interacts with target cell membranes and promotes membrane fusion. The free peptide catalyzes vesicle fusion at least to the lipid mixing stage and serves as a useful model fusion system. For gp41 constructs which lack the HFP, high-resolution structures show trimeric protein and suggest that at least three HFPs interact with the membrane with their C-termini in close proximity. In addition, previous studies have demonstrated that HFPs which are cross-linked at their C-termini to form trimers (HFPtr) catalyze fusion at a rate which is 15−40 times greater than noncross-linked HFP. In the present study, the structure of membrane-associated HFPtr was probed with solid-state nuclear magnetic resonance (NMR) methods. Chemical shift and intramolecular 13 CO-15 N distance measurements show that the conformation of the Leu-7 to Phe-11 region of HFPtr has predominant helical conformation in membranes without cholesterol and β strand conformation in membranes containing ∼30 mol% cholesterol. Interstrand 13 CO-13 CO and 13 CO-15 N distance measurements were not consistent with an in-register parallel strand arrangement but were consistent with either: (1) parallel arrangement with adjacent strands tworesidues out-of-register; or (2) antiparallel arrangement with adjacent strand crossing between Phe-8 and Leu-9. Arrangement (1) could support the rapid fusion rate of HFPtr because of placement of the apolar N-terminal regions of all strands on the same side of the oligomer while arrangement (2) could support the assembly of multiple fusion protein trimers. KeywordsHIV; fusion peptide; cholesterol; membranes; NMR; trimer Enveloped viruses such as human immunodeficiency virus (HIV) are surrounded by a membrane and infect cells through fusion between the viral membrane and the target cell membrane (1,2). This process is mediated by envelope proteins which traverse the viral membrane (3). For HIV, the gp41 envelope protein has a ∼170-residue ectodomain region † This work was supported by NIH award AI47153 to D. P. W. * To whom correspondence should be addressed. Telephone: 517−355−9715. Fax: 517−353−1793. Email: weliky@chemistry.msu.edu.. SUPPORTING INFORMATION AVAILABLE Equations are derived for determination of (ΔS/S 0 ) cor for REDOR and fpCTDQBU analyses. This material is available free of charge via the Internet at http://pubs.acs.org. NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2008 October 20. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript which lies outside the viral membrane and contains a N-terminal ∼20-residue apolar "fusion peptide" (HFP). The HFP interacts with the target cell membrane and plays an essential role in membrane fusion (4). Peptides composed of the HFP sequence induce fusion between large unilamellar vesicles (LUVs) and between erythrocytes (5,6). There are similar mutation/fusion activity relationships...

Fe 3 GeTe 2 has emerged as one of the most fascinating van der Waals crystals due to its two-dimensional (2D) itinerant ferromagnetism, topological nodal lines and Kondo lattice behavior. However, lattice dynamics, chirality of phonons and spin-phonon coupling in this material, which set the foundation for these exotic phenomena, have remained unexplored. Here we report the first experimental investigation of the phonons and mutual interactions between spin and lattice degrees of freedom in few-layerFe 3 GeTe 2 . Our results elucidate three prominent Raman modes at room temperature: two A 1g (Γ) and one E 2g (Γ) phonons. The doubly degenerate E 2g (Γ) mode reverses the helicity of incident photon, indicating the pseudo-angular momentum and chirality. Through analysis of temperature-dependent phonon energies and lifetimes, which strongly diverge from the anharmonic model below Curie temperature, we determine the spin-phonon coupling in Fe 3 GeTe 2 . Such interaction between lattice oscillations and spin significantly enhances the Raman susceptibility, allowing us to observe two additional Raman modes at the cryogenic temperature range. In addition, we reveal laser radiation induced degradation of Fe 3 GeTe 2 in ambient conditions and the corresponding Raman fingerprint. Our results provide the first experimental analysis of phonons in this novel 2D itinerant ferromagnet and their applicability for further fundamental studies and application development.