Biological Physics is an interdisciplinary field involving the application of the principles and techniques of experimental physics, biochemistry, and molecular biology to understand how biomolecules function and to characterize, manipulate, and modify living systems. Well-qualified graduate students are eligible for full support and training through an NIH-sponsored Molecular Biophysics Training Program.
- Biomembrane Technology and Biomolecular Photonics
The design of a new generation of materials based on biomembrane components holds promise in diverse areas including optical recording media, chemical sensors, nanometer lithography, energy transducers, and enzyme catalysts. A variety of membrane proteins, including bacteriorhodopsin, rhodopsin, and acetylcholine receptor, exhibit active properties such as energy transduction, active and passive transport, chemical sensing, voltage channel gating, signal transduction, and self-assembly, which could find important uses in such materials. However, future progress will depend on the development of new methods for engineering such biomolecules with properties including enhanced stability and the ability to exist in a solid-state environment so that they are suitable for use in biomolecular devices.
In this project, the biophysics group is developing new methods based on molecular genetics and advanced biophysical techniques that will provide the capability to modify membrane proteins at the molecular level. Key among these techniques will be site-directed non-native amino acid replacement (SNAAR). This approach will provide a new dimension in protein engineering, enabling the replacement of native amino acid residues with custom designed residues. Current studies are aimed at incorporating photoactive non-native residues that will alter the electro-optical properties of bacteriorhodopsin. In this regard, recent studies have demonstrated that films produced from bacteriorhodopsin can be used for optical information processing.
The group has also demonstrated recently that self-assembled biomembranes can be used as molecular templates for nanostructure material fabrication. In one set of experiments, in collaboration with N. Clark and K. Douglas at the University of Colorado, 2-dimensionally crystalline S-layers were used as templates to produce patterned thin metal films with nanometer-sized holes and wires. In a different study (in collaboration with C. Safinya at the University of California Santa Barbara), the group recently reported the discovery that dry films of bacteriorhodopsin are structurally stable up to 140oC. Studies are being conducted to produce heatproof arrays of other proteins.
- Energy Transduction, Ion Transport, and Signal Recognition
Membrane proteins facilitate many key cellular processes, including energy transduction, ion transport, and signal recognition. Because these proteins are often difficult to crystallize for x-ray analysis, little is known about their structures and molecular mechanisms. For this reason, a combination of advanced spectroscopic and recombinant DNA techniques are being developed to investigate how these membrane proteins function.
A key focus of research is the light-driven proton pump, bacteriorhodopsin. Since the early 1970’s, this protein has become a focus for understanding the molecular mechanisms of active ion transport and energy transduction in biological systems. Two other proteins being investigated are rhodopsin, the primary receptor in vision, and acetylcholine receptor, which is involved in the transmission of the nerve impulses.
A central approach is the use of Fourier transform infrared (FTIR) difference spectroscopy. The group has shown that this method can be used to detect small conformational changes in membrane proteins. By combining this approach with site-directed mutagenesis, they have been able to construct a model for the key molecular events that occur during proton pumping in bacteriorhodopsin. A more advanced method for assigning bands and conducting structure-function studies which involves the site-directed isotope labeling of proteins using in vitro expression and supressor tRNAs is also under development. In a related approach, the substitution of non-native amino acids is being used to produce new forms of membrane proteins that will be useful in biotechnology.
- Experimental Studies of Gels
Rama Bansil’s primary interest is in gels, which are found in numerous products of daily use, have fascinating visco-elastic properties, fundamentally different than solids or liquids. Bansil’s laboratory is devoted to interdisciplinary research ranging from Polymer Physics to Biophysics. Through a variety of experimental methods such as light scattering, small-angle X-ray and neutron scattering, and microscopy complemented by computer simulations of model gels, Bansil’s group has elucidated the structure of gels at the molecular level, the physics of gel formation, diffusion in gels and the kinetics of phase transitions and chemical reactions in gels. Current research projects include the phase behavior of multiblock copolymer gels and their application to develop templates for nanoscale devices. Many living tissues are in the form of gels, which has excited a great deal of interest as a substrate for tissue regeneration. Bansil and her collaborators at Harvard Medical School have focused their attention on understanding the role that gelation of mucin (a glycoprotein found in the mucus layer) plays in preventing the stomach from being digested by the highly acidic gastric juice that it secretes. Their studies using dynamic light scattering and atomic force microscopy have contributed to a detailed mechanism of how mucin molecules gel under acidic conditions.
- Near-Field Infrared Microscopy
The Erramilli group works on developing high-resolution infrared microscopy for studying biological systems. Images with spatial and temporal information add to our understanding of these systems. Vibrational spectroscopy is an exquisitely sensitive tool for studying the many biomolecular systems that exhibit characteristic “fingerprint” absorption bands. Combining this sensitivity with microscopy allows the imaging of living systems without using stains or labels. But conventional infrared microscopy is limited to poor spatial resolution set by the diffraction limit associated with the longer wavelengths involved. Scanning near-field infrared microscopy is used to break the diffraction limit without sacrificing the spectral sensitivity. A variety of bright infrared sources are used – broadband synchrotron radiation, free electron lasers, ultra fast tunable infrared lasers, and quantum cascade lasers.
Using this system, the first ever high-resolution underwater infrared images of single living cells have been obtained. Images of single fibroblasts at wavelengths at which proteins, nucleic acids, and lipids absorb suggest that cell motion is associated with complex topological changes in the membrane.
Currently, time-resolved methods taking advantage of a tunable 100-fs laser are being used to do “vibrational lifetime” imaging in the mid-infrared region of the spectrum.
Vibrational dynamics of biomolecular systems are studied using femtosecond single color and two color pump-probe methods, and photon echo studies. Ultrafast studies on anesthetic molecules like nitrous oxide are aimed at solving the long-standing biological physics problem of how anesthetics act.
- Ultrafast Infrared Spectroscopy
Collaboration: Prof L. Ziegler, Chemistry; Prof Ken Rothschild, Physics; Prof M. K. Hong, Physics, Prof Feng Wang, Chemistry; Prof Richard Averitt, Physics
Graduate Students: Eric Pinnick, Logan Chieffo, Jeff Shattuck, Xihua Wang, Jason Amsden (PhD Jan 2008), Mikkel Jensen, Erica Raber
A multidisciplinary collaboration project that involves the development of an ultra fast multicolor infrared spectrometer in order to study interactions of light on fundamental biological molecules and systems.
- Single Color IR pump-probe experiments have been used to study the nature of the environment of the anesthetic gas nitrous oxide in water and model membranes. These represent the first utrafast studies on an anesthetic gas N2O, which appears to be exquisitely sensitive to the hydration state of the membrane system [with Prof Ziegler & Prof Rothschild]
- Studies on vibrational energy relaxation in water have identified a novel energy relaxation pathway, and the dynamics of the combination band [with Prof Ziegler]
- The experimental studies are combined with Molecular Dynamics simulations to identify the role of ordering of water in nanoconfined systems [with Prof Feng Wang & helpful discussions with Prof Stanley]
- Visible pump-IR probe studies are used to study photoactive proteins [Prof Rothschild] have shown that the protein backbone responds within 800 femtoseconds of photoexcitation. The studies the first time such a fast response in the protein backbone has been detected in a bacterial proteorhodosin system.
- 2-D IR femtosecond IR spectroscopy:Traditional (1D) infrared spectroscopy can, at best, obtain spectra on a nanosecond time scale, and the spectra contain ambiguously broad lineshapes, which cannot be interpreted. Utilizing multiple ultra fast pulses, varied both in time and frequency, spectra can be obtained on a timescale of several hundred femtoseconds. These multidimensional spectra provide a direct measurement of the mechanism that leads to line width broadening, as well as information on the vibrational couplings in the molecule. The data obtained can be used to determine between homogenous and inhomogeneous broadening and to monitor the structure of a molecule on a femtosecond timescale.
A spectra physics Hurricane titanium sapphire laser is used to generate 100 femtosecond pulses, which are tuned to the appropriate wavelength for experimental conditions using non-linear crystals and optical parametric amplifiers. A 64-element HgCdTe array detector is used to study the spectrum over the full bandwidth of the laser pulse.