Physics Faculty Publications

Unified Behavior of Alkali Core-Level Binding-Energy Shifts Induced by sp Metals

E. Lundgren et al. — Fri, 03 May 2013 06:11:26 PDT

Thin overlayers of Na, K, Rb, and Cs on different sp-metal substrates have been investigated using photoelectron spectroscopy. The alkali core levels show clearly resolved binding-energy shifts between the surface layer, the intermediate layer(s), and the interface layer. The magnitude of these shifts depends on sp metal and on alkali metal. The layer-resolved core-level binding-energy shifts are well reproduced by models based on a thermodynamical description. For three-layer alkali films the core-level binding energy of the intermediate layer is found to exhibit a small but significant shift between different sp-metal substrates. A simple relationship between the core-level binding-energy shift for the interface layer and the difference in r_svalue between the sp substrate and the adsorbate is shown to exist. [S0163-1829(97)07443-2]

X-ray Standing-Wave Investigation of (1X2)Rb/Cu(110)

David R. Heskett et al. — Fri, 03 May 2013 06:01:40 PDT

We have carried out a back-reflection x-ray standing-wave (BRXSW)investigation to study the adsorbate ordering in the system (1X2)Rb/Cu(110), which corresponds to an alkali-induced missing row reconstruction of the Cu(110)surface. By carrying out measurements in three different scattering geometries, we find that for the missing row structure at room temperature, the Rb adatoms are extremely well ordered in the direction perpendicular to the surface, show a high degree of ordering across the missing rows (e.g., the atoms are locked into the missing row troughs), but are highly disordered along the rows, similar to a one-dimensional lattice gas. We compare our results to the Rb/Cu(110)-saturated surface at room temperature and to our previous BRXSW investigation of Rb/Cu(111).

Evidence of Inter- and Intra-Molecular Crosslinking of Tyrosine Residues of Calmodulin Induced by Photo-Activation of Ruthenium(II)

Oleg A. Andreev et al. — Tue, 12 Mar 2013 09:40:26 PDT

A Monomeric Membrane Peptide that Lives in Three Worlds: In Solution, Attached to, and Inserted across Lipid Bilayers

Yana K. Reshetnyak et al. — Tue, 12 Mar 2013 09:40:25 PDT

The membrane peptide pH (low) insertion peptide (pHLIP) lives in three worlds, being soluble in aqueous solution at pH 7.4, binding to the surface of lipid bilayers, and inserting as a transbilayer helix at low pH. With low pH driving the process, pHLIP can translocate cargo molecules attached to its C-terminus via a disulfide and release them in the cytoplasm of a cell. Here we examine a key aspect of the mechanism, showing that pHLIP is monomeric in each of its three major states: soluble in water near neutral pH (state I), bound to the surface of a membrane near neutral pH (state II), and inserted across the membrane as an α-helix at low pH (state III). The peptide does not induce fusion or membrane leakage. The unique properties of pHLIP made it attractive for the biophysical investigation of membrane protein folding in vitro and for the development of a novel class of delivery peptides for the transport of therapeutic and diagnostic agents to acidic tissue sites associated with various pathological processes in vivo.

Polarization of Fluorescently Labeled Myosin Subfragment-1 Fully or Partially Decorating Muscle Fibers and Myofibrils

Oleg A. Andreev et al. — Tue, 12 Mar 2013 09:40:24 PDT

Fluorescently labeled myosin heads (Si) were added to muscle fibers and myofibrils at various concentrations.The orientation of the absorption dipole of the dye with respect to the axis of F-actin was calculated from polarization of fluorescence which was measured by a novel method from video images of muscle. In this method light emitted from muscle was split by a birefringent crystal into two nonoverlapping images: the first image was created with light polarized in the direction parallel to muscle axis, and the second image was created with light polarized in the direction perpendicular to muscle axis. Images were recorded by high-sensitivity video camera and polarization was calculated from the relative intensity of both images. The method allows measurement of the fluorescence polarization from single myofibril irrigated with low concentrations of S1 labeled with dye. Orientation was also measured by fluorescence-detected linear dichroism. The orientation was different when muscle was irrigated with high concentration of S1 (molar ratio S1 :actin in the I bands equal to 1) then when it was irrigated with low concentration of S1 (molar ratio S1 :actin in the I bands equal to 0.32). The results support our earlier proposal that S1 could form two different rigor complexes with F-actin depending on the molar ratio of S1 :actin.

Folding Kinetics and Structure of OEP16

Dirk Linke et al. — Tue, 12 Mar 2013 09:40:23 PDT

The chloroplast outer membrane contains different, specialized pores that are involved in highly specific traffic processes from the cytosol into the chloroplast and vice versa. One representative member of these channels is the outer envelope protein 16 (OEP16), a cation-selective high conductance channel with high selectivity for amino acids. Here we study the mechanism and kinetics of the folding of this membrane protein by fluorescence and circular dichroism spectroscopy, using deletion mutants of the two single tryptophanes Trp-77->Phe-77 and Trp-100->Phe-100. In addition, the wild-type spectra were deconvoluted, depicting the individual contributions from each of the two tryptophan residues. The results show that bothtryptophan residues are located in a completely different environment. The Trp-77 is deeply buried in the hydrophobic part of the protein, whereas the Trp-100 is partially solvent exposed. These results were further confirmed by studies of luorescence quenching with I^-. The kinetics of the protein folding are studied by stopped flow fluorescence and circular dichroism measurements. The folding process depends highly on the detergent concentration and can be divided into an ultrafast phase (k > 000 s^-¹), a fast phase (200–800 s^-¹), and a slow phase (25–70 s^-¹). The slow phase is absent in the W100F mutant. Secondary structure analysis and comparision with closely related proteins led to a new model of the structure of OEP16, suggesting that the protein is, in contrast to most other outer membrane proteins studied so far, purely α-helical, consisting of four transmembrane helices. Trp-77 is located in helix II, whereas the Trp-100 is located in the loop between helices II and III,close to the interface to helix III. We suggest that the first, very fast process corresponds to the formation of the helices, whereas the insertion of the helices into the detergent micelle and the correct folding of the II-III loop may be the later, rate-limiting steps of the folding process.

Decomposition of Protein Tryptophan Fluorescence Spectra into Log- Normal Components. III. Correlation between Fluorescence and Microenvironment Parameters of Individual Tryptophan Residues

Yana K. Reshetnyak et al. — Tue, 12 Mar 2013 09:35:16 PDT

In our previous paper (Reshetnyak, Ya. K., and E. A. Burstein. 2001. Biophys. J. 81:1710–1734) we confirmed the existence of five statistically discrete classes of emitting tryptophan fluorophores in proteins. The differences in fluorescence properties of tryptophan residues of these five classes reflect differences in interactions of excited states of tryptophan fluorophores with their microenvironment in proteins. Here we present a system of describing physical and structural parameters of microenvironments of tryptophan residues based on analysis of atomic crystal structures of proteins. The application of multidimensional statistical methods of cluster and discriminant analyses for the set of microenvironment parameters of 137 tryptophan residues of 48 proteins with known three-dimensional structures allowed us to 1) demonstrate the discrete nature of ensembles of structural parameters of tryptophan residues in proteins; 2) assign spectral components obtained after decomposition of tryptophan fluorescence spectra to individual tryptophan residues; 3) find a correlation between spectroscopic and physico-structural features of the microenvironment; and 4) reveal differences in structural and physical parameters of the microenvironment of tryptophan residues belonging to various spectral classes.

Decomposition of Protein Tryptophan Fluorescence Spectra intoLog-Normal Components. II. The Statistical Proof of Discreteness ofTryptophan Classes in Proteins

Yana K. Reshetnyak et al. — Tue, 12 Mar 2013 09:35:15 PDT

The physical causes for wide variation of Stokes shift values in emission spectra of tryptophan fluorophores in proteins have been proposed in the model of discrete states (Burstein, E. A., N. S. Vedenkina, and M. N. Ivkova. 1973. Photochem. Photobiol. 18:263–279; Burstein, E. A. 1977a. Intrinsic Protein Luminescence (The Nature and Application). In Advances in Science and Technology (Itogi Nauki i Tekhniki), Biophysics Vol. 7. VINITI, Moscow [In Russian]; Burstein, E. A. 1983. Molecular Biology (Moscow) 17:455–467 [In Russian; English translation]). It was assumed that the existence of the five most probable spectral classes of emitting tryptophan residues and differences among the classes were analyzed in terms of various combinations of specific and universal interactions of excited fluorophores with their environment. The development of stable algorithms of decomposition of tryptophan fluorescence spectra into log-normal components gave us an opportunity to apply two mathematically different algorithms, SImple fitting with Mean-Square criterion (SIMS) and PHaseplot- based REsolving with Quenchers (PHREQ) for the decomposition of a representative set of emission spectra of proteins.Here we present the results of decomposition of tryptophan emission spectra of > 100 different proteins, some in various structural states (native and denatured, in complexes with ions or organic ligands, in various pH-induced conformations, etc.). Analysis of the histograms of occurrence of >300 spectral log-normal components with various maximum positions confirmed the statistical discreteness of several states of emitting tryptophan fluorophores in proteins.

Decomposition of Protein Tryptophan Fluorescence Spectra into Log-Normal Components. I. Decomposition Algorithms

Edward A. Burstein et al. — Tue, 12 Mar 2013 09:35:14 PDT

Two algorithms of decomposition of composite protein tryptophan fluorescence spectra were developed based on the possibility that the shape of elementary spectral component could be accurately described by a uniparametric log-normal function. The need for several mathematically different algorithms is dictated by the fact that decomposition of spectra into widely overlapping smooth components is a typical incorrect problem. Only the coincidence of components obtained with various algorithms can guarantee correctness and reliability of results. In this paper we propose the following algorithms of decomposition: (1) the SImple fitting procedure using the root-Mean- Square criterion (SIMS) operating with either individual emission spectra or sets of spectra measured with various quencher concentrations; and (2) the pseudo-graphic analytical procedure using a PHase plane in coordinates of normalized emission intensities at various wavelengths (wavenumbers) and REsolving sets of spectra measured with various Quencher concentrations (PHREQ). The actual experimental noise precludes decomposition of protein spectra into more than three components.

A Monomeric Membrane Peptide that Lives in Three Worlds: In Solution,Attached to, and Inserted across Lipid Bilayers

Yana K. Reshetnyak et al. — Tue, 12 Mar 2013 09:15:26 PDT

The membrane peptide pH (low) insertion peptide (pHLIP) lives in three worlds, being soluble in aqueous solution at pH 7.4, binding to the surface of lipid bilayers, and inserting as a transbilayer helix at low pH. With low pH driving the process, pHLIP can translocate cargo molecules attached to its C-terminus via a disulfide and release them in the cytoplasm of a cell. Here we examine a key aspect of the mechanism, showing that pHLIP is monomeric in each of its three major states: soluble in water near neutral pH (state I), bound to the surface of a membrane near neutral pH (state II), and inserted across the membrane as an a-helix at low pH (state III). The peptide does not induce fusion or membrane leakage. The unique properties of pHLIP made it attractive for the biophysical investigation of membrane protein folding in vitro and for the development of a novel class of delivery peptides for the transport of therapeutic and diagnostic agents to acidic tissue sites associated with various pathological processes in vivo.

Bilayer Interactions of pHLIP, a Peptide that Can Deliver Drugs and Target Tumors

Manuela Zoonens et al. — Tue, 12 Mar 2013 09:15:25 PDT

The pH-dependent insertion of pHLIP across membranes is proving to be a useful property for targeting acidic tissues or tumors and delivering drugs attached to its C-terminus. It also serves as a model peptide for studies of protein insertion into membranes, so further elucidation of the insertion mechanism of pHLIP and its features is desirable. We examine how the peptide perturbs a model phosphatidylcholine membrane and how it associates with the lipid bilayer using an array of fluorescence techniques, including fluorescence anisotropy measurements of TMA-DPH anchored in bilayers, quenching of pHLIP fluorescence by brominated lipids and acrylamide, and measurements of energy transfer between aromatic residues of pHLIP and TMA-DPH. When pHLIP is bound to the surface of bilayers near neutral pH, the membrane integrity is preserved whereas the elastic properties of bilayers are changed as reported by an increase of membrane viscosity. When it is inserted, there is little perturbation of the lipids. The results also suggest that pHLIP can bind to the membrane surface in a shallow or a deep mode depending on the phase state of the lipids. Using parallax analysis, the change of the penetration depth of pHLIP was estimated to be 0.4 Å from the bilayer center and 2.8 Å from the membrane surface after the liquid-to-gel phase transition.

Ultracold Neutron Depolarization in Magnetic Bottles

A. Steyerl et al. — Fri, 08 Mar 2013 11:20:17 PST

We analyze the depolarization of ultracold neutrons confined in a magnetic field configuration similar to those used in existing or proposed magnetogravitational storage experiments aiming at a precise measurement of the neutron lifetime.We use an extension of the semiclassical Majorana approach as well as an approximate quantum mechanical analysis, both pioneered by Walstrom et al. [Nucl. Instrum. Methods Phys. Res. A 599, 82 (2009)]. In contrast with this previous work we do not restrict the analysis to purely vertical modes of neutron motion. The lateral motion is shown to cause the predominant depolarization loss in a magnetic storage trap. The system studied also allowed us to estimate the depolarization loss suffered by ultracold neutrons totally reflected on a nonmagnetic mirror immersed in amagnetic field. This problem is of preeminent importance in polarized neutron decay studies such as the measurement of the asymmetry parameter A using ultracold neutrons, and it may limit the efficiency of ultracold neutron polarizers based on passage through a high magnetic field.

Accurate Analysis of Tumor Margins Using a Fluorescent pH Low Insertion Peptide (pHLIP)

James Segala et al. — Fri, 15 Feb 2013 09:05:16 PST

The recurrence of certain cancers remains quite high due to either incomplete surgical removal of the primary tumor or the presence of small metastases that are invisible to the surgeon. Near infrared (NIR) fluorescence imaging might improve surgical outcomes by providing sensitive, specific, and real-time visualization of normal and diseased tissues if agents can be found that discriminate between normal and diseased tissue and define tumor margins. We have developed a new approach for revealing tumor borders by using NIR fluorescently labeled pH Low Insertion Peptide (pHLIP) and have created a computational program for the quantitative assessment of tumor boundaries. The approach is tested in vivo by co-localization of GFP-tumors and NIR emission from the fluorescently labeled pHLIP, and it is found that boundaries are accurately reported and that sub-millimeter masses can be detected.

Quantum Monte Carlo Methods in Statistical Mechanics

Vilen Melik-Alaverdian et al. — Mon, 04 Feb 2013 10:12:14 PST

This paper deals with the optimization of trial states for the computation of dominant eigenvalues of operators and very large matrices. In addition to preliminary results for the energy spectrum of van der Waals clusters, we review results of the application of this method to the computation of relaxation times of independent relaxation modes at the Ising critical point in two dimensions.

Quasielastic scattering in the interaction of ultracold neutrons with a liquid wall and application in a reanalysis of the Mambo I neutron-lifetime experiment

Charles Kaufman et al. — Mon, 12 Nov 2012 14:45:19 PST

A Dynamical Definition of Atomic Clusters

J. Xie et al. — Fri, 31 Aug 2012 12:05:17 PDT

Summary of the Workshop on the Applications of X-Ray Standing Waves in Studies of Surfaces, FiIms, and BuIk MateriaIs

David R. Heskett et al. — Fri, 31 Aug 2012 11:55:14 PDT

Highlights of the satellite workshop on the technique of x-ray standing waves which preceded the 5th International Conference on Synchrotron Radiation Instrumentation held at the State University of New York at Stony Brook, USA are presented. At the workshop, many applications of the x-ray standing-wave technique were described in both invited and contributed talks. While the predominant use of the XSW technique was to analyze the structure of adsorbates on surfaces, applications in the characterization of thin films, interfaces, clean surfaces, and bulk materials were also presented. Most of the talks concentrated on experimental results, but some theory was also featured.

X-Ray Standing-Wave Investigations of Valence Electronic Structure

J. C. Woicik et al. — Fri, 31 Aug 2012 11:55:12 PDT

We have examined the valence-electron emission from Cu, Ge, GaAs, InP, and NiO single crystals under the condition of strong x-ray Bragg reflection; i.e., in the presence of the spatially modulated x-ray standing-wave interference field that is produced by the superposition of the incident and reflected x-ray beams. These crystals span the entire metallic, covalent, and ionic range of solid-state bonding. It is demonstrated that the valenceelectron emission is closely coupled to the atomic cores, even for electron states close to a metallic Fermi edge. Using the bond-orbital approximation, the x-ray standing-wave structure factor for valence-electron emission is derived in terms of the bond polarities and photoionization cross sections of the atoms within the crystalline unit cell and compared to experiment. Additionally, we demonstrated that by exploiting the spatial dependence of the electric-field intensity under Bragg condition, site specific valence electronic structure may be obtained. The technique is demonstrated for GaAs and NiO.

Hybridization and Bond-Orbital Components in Site-Specific X-Ray Photoelectron Spectra of Rutile TiO2

J. C. Woicik et al. — Fri, 31 Aug 2012 11:45:12 PDT

We have determined the Ti and O components of the rutile TiO₂ valence band using the method of sitespecific x-ray photoelectron spectroscopy. Comparisons with calculations based on pseudopotentials within the local density approximation reveal the hybridization of the Ti 3d, 4s, and 4p states, and the O 2s and 2p states on each site. These chemical effects are observed due to the large differences between the angular-momentum dependent matrix elements of the photoelectron process.

Surface Roughness Effect on Ultracold Neutron Interaction With a Wall and Implications for Computer Simulations

A. Steyerl et al. — Fri, 31 Aug 2012 11:35:19 PDT

We review the diffuse scattering and the loss coefficient in ultracold neutron reflection from slightly rough surfaces, report a surprising reduction in loss coefficient due to roughness, and discuss the possibility of transition from quantum treatment to ray optics. The results are used in a computer simulation of neutron storage in a recent neutron lifetime experiment that reported a large discrepancy of neutron lifetime with the current particle data value. Our partial reanalysis suggests the possibility of systematic effects that were not included in this publication.