Graduate Student Seminar Scheduled for October 15

The Fall 2008 Beckman Institute Graduate Student Seminar series continues on Wednesday, October 15. The seminar will feature three short talks from graduate students Leonardo Trabuco, Wei Ye, and Xing Liang. 

The Beckman Institute Graduate Student Seminar Series presents the work of outstanding graduate students working in Beckman research groups. The seminar starts at Noon in Beckman Institute Room 1005 and is open to the public. Lunch will be served.

Ribosome-induced conformational changes in EF-Tu control GTP hydrolysis
Leonardo Trabuco

During translation, EF-Tu presents the aminoacyl-tRNA to the mRNA-programmed ribosome. Ribosome-induced GTPase activity of EF-Tu triggers conformational changes of the factor, that play a pivotal role in the selection and delivery of the cognate tRNA. A 6.7-Å resolution cryo-EM map of the aminoacyl-tRNA•EF-Tu•GDP•kir ternary complex-bound E. coli 70S ribosome reveals key conformational changes in the conserved switch regions of EF-Tu, which form a pocket for the gamma-phosphate of the guanosine nucleotide. Using a novel molecular dynamics-based flexible fitting method, a quasi-atomic model based on the EM data has been obtained. The model allows the characterization of the binding interaction between the factor and the ribosome at unprecedented detail, revealing the underlying molecular mechanism that triggers GTP hydrolysis in EF-Tu. The structural evidence supports the hydrophobic gate model, i.e., the suggestion that interaction with the ribosome opens a gate formed by residues Ile60 and Val20 which, when open, allows His84 to act as a general base activating an active-site nucleophilic water molecule, and thus triggering hydrolysis. Furthermore, the effector loop is observed to interact with a conserved rRNA region of the 30S subunit, likely corresponding to a transition state between the GTP and GDP forms of the factor.

Direct writing of sub-5nm metallic hafnium diboride nanostructures by UHV-STM
Wei Ye

The patterning of metallic nanostructures on surfaces is of great interest in fabricating nanoelectronics and quantum devices. In this talk, we describe the fabrication and characterization of sub-5 nmmetallic hafnium diboride (HfB2) nanostructures on Si(100)2x1:Hsurfaces using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). HfB2 nanostructures are deposited on silicon surfaces by STM-assisted chemical vapor deposition (CVD) from the single-source precursor Hf(BH4)4 at room temperature. The delivery of Hf(BH4)4 vapor is realized by pointing a capillary doser directly at the tip-sample junction. At positive sample bias, the tunneling current initiates the local CVD by the decomposition of Hf(BH4)4 under STM tip. By repeatedly scanning the STM tip along a specific path, well-defined HfB2 nanostructures can be directly written onto the surface. Spatially resolved tunneling current-voltage (I-V) spectroscopy is used to characterize the electronic properties of the nanostructures. We have achieved 4 nm linewidths and complete selectivity relative to adjacent H-Si(100) regions. The thickness of the nanostructures is controlled by the exposure time to the electron beam from STM tip, while the width is controlled only by the geometry of the tip apex and the sample-tip separation. STS data confirm that the HfB2 nanostructures deposited are purely metallic, indicating minimum contaminations in the nanostructures, which we attribute to the carbon-free nature of the CVD precursor. To our knowledge this is the first demonstration of sub-5 nm metallic nanostructures in a STM/CVD experiment.

Optical coherence elastography and its applications
Xing Liang

Biomechanical properties of living tissues depend on their molecular building blocks which can shape and modify the cellular and extracellular structures. For instance, pathological changes such as tumor invasion will lead to different biomechanical properties in tissues. Thus, tissue biomechanical properties are of great importance, as well as our ability to measure them on the micron-scale. To enable these measurements, a novel non-invasive, micron-scale and dynamic Optical Coherence Elastography (OCE) system has been developed utilizing a titanium:sapphire laser based spectral-domain Optical Coherence Tomography (OCT). This system provides an axial resolution of 3 microns, a transverse resolution of 13 microns, and an acquisition rate as high as 33,000 lines per second. External and internal mechanical excitations are applied to the samples in the system. By modeling the samples and solving wave equations, experimental results of OCE on tissue phantoms and human breast tumor tissues are obtained, which provide the quantitative elastic moduli of the samples. With micron-scale resolution and a high-speed acquisition rate, this OCE system also has the potential to rapidly measure dynamic in vivo 3-D tissue biomechanical properties.