Search PubMed⌕ Search

Biomedical subjects

Richard A Mathies

Publications and source records attributed to Richard A Mathies.

52 records · Page 3Linked to original sources

Retinal counterion switch in the photoactivation of the G protein-coupled receptor rhodopsin.

The biological function of Glu-181 in the photoactivation process of rhodopsin is explored through spectroscopic studies of site-specific mutants. Preresonance Raman vibrational spectra of the unphotolyzed E181Q mutant are nearly identical to spectra of the native pigment, supporting the view that Glu-181 is uncharged (protonated) in the dark state. The pH dependence of the absorption of the metarhodopsin I (Meta I)-like photoproduct of E181Q is investigated, revealing a dramatic shift of its Schiff base pKa compared with the native pigment. This result is most consistent with the assignment of Glu-181 as the primary counterion of the retinylidene protonated Schiff base in the Meta I state, implying that there is a counterion switch from Glu-113 in the dark state to Glu-181 in Meta I. We propose a model where the counterion switch occurs by transferring a proton from Glu-181 to Glu-113 through an H-bond network formed primarily with residues on extracellular loop II (EII). The resulting reorganization of EII is then coupled to movements of helix III through a conserved disulfide bond (Cys110-Cys187); this process may be a general element of G protein-coupled receptor activation.

Animals↗

Picosecond dynamics of G-protein coupled receptor activation in rhodopsin from time-resolved UV resonance Raman spectroscopy.

The protein response to retinal chromophore isomerization in the visual pigment rhodopsin is studied using picosecond time-resolved UV resonance Raman spectroscopy. High signal-to-noise Raman spectra are obtained using a 1 kHz Ti:Sapphire laser apparatus that provides <3 ps visible (466 nm) pump and UV (233 nm) probe pulses. When there is no time delay between the pump and probe events, tryptophan modes W18, W16, and W3 exhibit decreased Raman scattering intensity. At longer pump-probe time delays of +5 and +20 ps, both tryptophan (W18, W16, W3, and W1) and tyrosine (Y1 + 2xY16a, Y7a, Y8a) peak intensities drop by up to 3%. These intensity changes are attributed to decreased hydrophobicity in the microenvironment near at least one tryptophan and one tyrosine residue that likely arise from weakened interaction with the beta-ionone ring of the chromophore following cis-to-trans isomerization. Examination of the crystal structure suggests that W265 and Y268 are responsible for these signals. These UV Raman spectral changes are nearly identical to those observed for the rhodopsin-to-Meta I transition, implying that impulsively driven protein motion by the isomerizing chromophore during the 200 fs primary transition drives key structural changes that lead to protein activation.

Animals↗

Homogeneous immunoassay for detection of TNT and its analogues on a microfabricated capillary electrophoresis chip.

A homogeneous immunoassay for TNT and its analogues is developed using a microfabricated capillary electrophoresis chip. The assay is based on the rapid electrophoretic separation of an equilibrated mixture of an anti-TNT antibody, fluorescein-labeled TNT, and unlabeled TNT or its analogue. The band intensities of the free fluorescein-labeled TNT and of the antibody-antigen complex reveal the relative equilibrated concentrations. Titration of the anti-TNT antibody with a fluorescein-labeled TNT derivative yields a binding constant of (3.9 +/- 1.3) x 10(9) M(-1). The dissociation rate constant of the complex is determined by kinetic capillary electrophoresis using a folded channel and a rotary scanner to interrogate the separation at multiple time points. The dissociation rate constant is found to be 0.035 +/- 0.005 s(-1), and the resulting binding rate constant is (1.4 +/- 0.7) x 10(7) M(-1) s(-1). Binding constants of TNT and five of its analogues are determined by competitive assays: TNT (4.3 +/- 2.6) x 10(8) M(-1); 1,3,5-trinitrobenzene (5.1 +/- 3.3) x 10(7) M(-1); picric acid (7.5 +/- 4.4) x 10(6) M(-1); 2,4-dinitrotoluene (7.9 +/- 4.0) x 10(6) M(-1); 1,3-dinitrobenzene (1.0 +/- 0.7) x 10(6) M(-1); and 2,4-dinitrophenol (5.1 +/- 3.0) x 10(4) M(-1). TNT and its analogues can be assayed with high sensitivity (LOD 1 ng/mL) and with a wide dynamic range (1-300 ng/mL) using this chip-based method.

Algorithms↗

Structure of the aqueous solvated electron from resonance Raman spectroscopy: lessons from isotopic mixtures.

The structure and thermodynamics of the hydrated electron are probed with resonance Raman spectroscopy of isotopic mixtures of H(2)O and D(2)O. The strongly enhanced intramolecular bends of e(-)(H(2)O) and e(-)(D(2)O) produce single downshifted bands, whereas the e(-)(HOD) bend consists of two components: one slightly upshifted from the 1,446 cm(-1) bulk frequency to 1,457 cm(-1) and the other strongly downshifted to approximately 1,396 cm(-1). This 60 cm(-1) split and the 200 (120) cm(-1) downshifts of the OH (OD) stretch frequencies relative to bulk water reveal that the water molecules that are Franck-Condon coupled to the electron are in an asymmetric environment, with one proton forming a strong hydrogen bond to the electron. The downshifted bend and librational frequencies also indicate significantly weakened torsional restoring forces on the water molecules of e(-)(aq), which suggests that the outlying proton is a poor hydrogen bond donor to the surrounding solvent. A 1.6-fold thermodynamic preference of the electron for H(2)O is observed based on the relative intensities of the e(-)(H(2)O) and e(-)(D(2)O) bands in a 50:50 isotopic mixture. This equilibrium isotope effect is consistent with the downshifted vibrational frequencies and a relative reduction of the zero-point energy of H(2)O bound to the electron. Our results enhance the cavity model of the solvated electron and support only those models that contain water monomers as opposed to other molecular species.

Journal Article↗

Analysis of the mode-specific excited-state energy distribution and wavelength-dependent photoreaction quantum yield in rhodopsin.

The photoreaction quantum yield of rhodopsin is wavelength dependent: phi(lambda) is reduced by up to 5% at wavelengths to the red of 500 nm but is invariant (phi = 0.65 +/- 0.01) between 450 and 500 nm (Kim et al., 2001). To understand this nonstatistical internal conversion process, these results are compared with predictions of a Landau-Zener model for dynamic curve crossing. The initial distribution of excess photon energy in the 28 Franck-Condon active vibrational modes of rhodopsin is defined by a fully thermalized sum-over-states vibronic calculation. This calculation reveals that absorption by high-frequency unreactive modes (e.g., C[double bond]C stretches) increases as the excitation wavelength is shifted from 570 to 450 nm whereas relatively less energy is deposited into reactive low-frequency modes. This result qualitatively explains the experimentally observed wavelength dependence of phi(lambda) for rhodopsin and reveals the importance of delocalized, torsional modes in the reactive pathway.

Computer Simulation↗

Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis.

Modern DNA sequencing 'factories' have revolutionized biology by completing the human genome sequence, but in the race to completion we are left with inefficient, cumbersome, and costly macroscale processes and supporting facilities. During the same period, microfabricated DNA sequencing, sample processing and analysis devices have advanced rapidly toward the goal of a 'sequencing lab-on-a-chip'. Integrated microfluidic processing dramatically reduces analysis time and reagent consumption, and eliminates costly and unreliable macroscale robotics and laboratory apparatus. A microfabricated device for high-throughput DNA sequencing that couples clone isolation, template amplification, Sanger extension, purification, and electrophoretic analysis in a single microfluidic circuit is now attainable.

Base Sequence↗

Polymorphism ratio sequencing: a new approach for single nucleotide polymorphism discovery and genotyping.

Polymorphism ratio sequencing (PRS) combines the advantages of high-throughput DNA sequencing with new labeling and pooling schemes to produce a powerful assay for sensitive single nucleotide polymorphism (SNP) discovery, rapid genotyping, and accurate, multiplexed allele frequency determination. In the PRS method, dideoxy-terminator extension ladders generated from a sample and reference template are labeled with different energy-transfer fluorescent dyes and coinjected into a separation capillary for comparison of relative signal intensities. We demonstrate the PRS method by screening two human mitochondrial genomes for sequence variations using a microfabricated capillary array electrophoresis device. A titration of multiplexed DNA samples places the limit of minor allele frequency detection at 5%. PRS is a sensitive and robust polymorphism detection method for the analysis of individual or multiplexed samples that is compatible with any four-color fluorescence DNA sequencer.

Codon↗

Femtosecond broadband stimulated Raman: a new approach for high-performance vibrational spectroscopy.

Femtosecond stimulated Raman spectroscopy (FSRS) is a new technique that produces high-quality vibrational spectra free from background fluorescence. FSRS combines a narrow-bandwidth picosecond Raman pump pulse with an approximately 80 fs continuum probe pulse to produce stimulated Raman spectra from the pump-induced gain in the probe spectrum. The high intensity of the Raman pump combined with the broad bandwidth of the probe produces high signal-to-noise vibrational spectra with very short data acquisition times. FSRS spectra of standard solutions and solvents such as aqueous Na2SO4, aqueous KNO3, methanol, isopropanol, and cyclohexane are collected in seconds. Furthermore, stimulated Raman spectra can be obtained using just a single pump-probe pulse pair that illuminates the sample for only approximately 1 ps. Fluorescence rejection is demonstrated by collecting FSRS spectra of dyes (rhodamine 6G, chlorophyll a, and DTTCI) with varying degrees of fluorescence background and resonance enhancement. The high signal-to-noise, short data acquisition time, fluorescence rejection, and high spectral and temporal resolution of femtosecond stimulated Raman spectroscopy make it a valuable new vibrational spectroscopic technique.

Artifacts↗

Microfabricated 384-lane capillary array electrophoresis bioanalyzer for ultrahigh-throughput genetic analysis.

A microfabricated 384-lane capillary array electrophoresis device is developed and utilized for massively parallel genetic analysis. The 384 capillary lanes, arrayed radially about the center of a 200-mm-diameter glass substrate sandwich, are constructed using scalable microfabrication techniques derived from the semiconductor industry. Samples are loaded into reservoirs on the perimeter of the wafer, separated on the 8-cm-long poly(dimethylacrylamide) gel-filled channels, and detected with a four-color rotary confocal fluorescence scanner. The performance and throughput of this bioanalyzer are demonstrated by simultaneous genotyping 384 individuals for the common hemochromatosis-linked H63D mutation in the human HFE gene in only 325 s. This lab-on-a-chip device thoroughly exploits the power of microfabrication to produce high-density capillary electrophoresis arrays and to use them for high-throughput bioanalysis.

DNA↗

Microchip bioprocessor for integrated nanovolume sample purification and DNA sequencing.

A microfabricated electrophoretic bioprocessor for integrated DNA sequencing sample desalting, template removal, preconcentration, and CE analysis is presented. A low-viscosity gel capture matrix, containing an acrylamide-copolymerized oligonucleotide complementary to the 20-base sequence directly 3' of the M13-40 universal forward priming site, is introduced into the 60-nL capture chamber. Unpurified DNA sequencing reaction products are electrophoretically driven through the chamber; extension products hybridize to the matrix, while contaminating buffering ions, Cl-, excess primer, and template DNA are unretained. Purification under optimized conditions is complete in only 120 s (binding temperature 50 degrees C, driving voltage 250 V). High-speed, integrated sequencing analysis is accomplished by releasing the gel-purified duplex at 67 degrees C and directly injecting onto a 15.9-cm effective length CE microchannel. Electrophoretic resolution of the sequencing products is complete in 32 min, producing a total of 560 bp with phred quality q > or = 20 (accuracy > or = 99%). This fully integrated nanoliter process decreases the purification time approximately 10-fold and the process volume approximately 100-fold while providing state-of-the-art sequencing results.

Algorithms↗

Anti-stokes Raman study of vibrational cooling dynamics in the primary photochemistry of rhodopsin.

Picosecond Stokes and anti-Stokes Raman spectra are used to probe the structural dynamics and reactive energy flow in the primary cis-to-trans isomerization reaction of rhodopsin. The appearance of characteristic ethylenic, hydrogen out-of-plane (HOOP), and low-wavenumber photoproduct bands in the Raman spectra is instrument-response-limited, consistent with a subpicosecond product appearance time. Intense high and low-frequency anti-Stokes peaks demonstrate that the all-trans photoproduct is produced vibrationally hot on the ground-state surface. Specifically, the low-frequency modes at 282, 350, and 477 cm(-1) are highly vibrationally excited (T > 2000 K) immediately following isomerization, revealing that these low-frequency motions directly participate in the reactive curve-crossing process. The anti-Stokes modes are characterized by a approximately 2.5 ps temporal decay that coincides with the conversion of photorhodopsin to bathorhodopsin. This correspondence shows that the photo-to-batho transition is a ground-state cooling process and that energy storage in the primary visual photoproduct is complete on the picosecond time scale. Finally, unique Stokes vibrations at 290, 992, 1254, 1290, and 1569 cm(-1) arising from the excited state of rhodopsin are observed only at 0 ps delay.

Journal Article↗

Time-resolved resonance Raman analysis of chromophore structural changes in the formation and decay of rhodopsin's BSI intermediate.

Time-resolved resonance Raman microchip flow experiments are performed to obtain the vibrational spectrum of the chromophore in rhodopsin's BSI intermediate and to probe structural changes in the bathorhodopsin-to-BSI and BSI-to-lumirhodopsin transitions. Kinetic Raman spectra from 250 ns to 3 micros identify the key vibrational features of BSI. BSI exhibits relatively intense HOOP modes at 886 and 945 cm(-1) that are assigned to C(14)H and C(11)H=C(12)H A(u) wags, respectively. This result suggests that in the bathorhodopsin-to-BSI transition the highly strained all-trans chromophore has relaxed in the C(10)-C(11)=C(12)-C(13) region, but is still distorted near C(14). The low frequency of the 11,12 A(u) HOOP mode in BSI compared with that of lumirhodopsin and metarhodopsin I indicates weaker coupling between the 11H and 12H wags due to residual distortion of the BSI chromophore near C(11)=C(12). The C=NH(+) stretching mode in BSI at 1653 cm(-1) exhibits a normal deuteriation induced downshift of 23 cm(-1), implying that there is no significant structural rearrangement of the Schiff base counterion region in the transition of bathorhodopsin to BSI. However, a dramatic Schiff base environment change occurs in the BSI-to-lumirhodopsin transition, because the 1638 cm(-1) C=NH(+) stretching mode in lumirhodopsin is unusually low and shifts only 7 cm(-1) in D(2)O, suggesting that it has essentially no H-bonding acceptor. With these data we can for the first time compare and discuss the room temperature resonance Raman vibrational structure of all the key intermediates in visual excitation.

Animals↗

Function of extracellular loop 2 in rhodopsin: glutamic acid 181 modulates stability and absorption wavelength of metarhodopsin II.

The second extracellular loop of rhodopsin folds back into the membrane-embedded domain of the receptor to form part of the binding pocket for the 11-cis-retinylidene chromophore. A carboxylic acid side chain from this loop, Glu181, points toward the center of the retinal polyene chain. We studied the role of Glu181 in bovine rhodopsin by characterizing a set of site-directed mutants. Sixteen of the 19 single-site mutants expressed and bound 11-cis-retinal to form pigments. The lambda(max) value of mutant pigment E181Q showed a significant spectral red shift to 508 nm only in the absence of NaCl. Other substitutions did not significantly affect the spectral features of the mutant pigments in the dark. Thus, Glu181 does not contribute significantly to spectral tuning of the ground state of rhodopsin. The most likely interpretation of these data is that Glu181 is protonated and uncharged in the dark state of rhodopsin. The Glu181 mutants displayed significantly increased reactivity toward hydroxylamine in the dark. The mutants formed metarhodopsin II-like photoproducts upon illumination but many of the photoproducts displayed shifted lambda(max) values. In addition, the metarhodopsin II-like photoproducts of the mutant pigments had significant alterations in their decay rates. The increased reactivity of the mutants to hydroxylamine supports the notion that the second extracellular loop prevents solvent access to the chromophore-binding pocket. In addition, Glu181 strongly affects the environment of the retinylidene Schiff base in the active metarhodopsin II photoproduct.

Animals↗

High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor.

High throughput DNA sequencing has been performed by using a microfabricated 96-channel radial capillary array electrophoresis (microCAE) microchannel plate detected by a 4-color rotary confocal fluorescence scanner. The microchannel plate features a novel injector for uniform sieving matrix loading as well as high resolution, tapered turns that provide an effective separation length of 15.9 cm on a compact 150-mm diameter wafer. Expanded common buffer chambers for the cathode, anode, and waste reservoirs are used to simplify electrode addressing and to counteract buffering capacity depletion arising from the high electrophoretic current. DNA sequencing data from 95 successful lanes out of 96 lanes run in parallel were batch-processed with basefinder, producing an average read length of 430 bp (phred q > or = 20). Phred quality values were found to exceed 40 (0.01% probability of incorrectly calling a base) for over 80% of the read length. The microCAE system demonstrated here produces sequencing data at a rate of 1.7 kbp/min, a 5-fold increase over current commercial capillary array electrophoresis technology. Additionally, this system permits lower reagent volumes and lower sample concentrations, and it presents numerous possibilities for integrated sample preparation and handling. The unique capabilities of microCAE technology should make it the next generation, high performance DNA sequencing platform.

Base Sequence↗

Fluorescence labeling methods for microchannel plate capillary electrophoresis DNA sizing.

DNA analysis on microchannel plate (MCP) capillary electrophoresis platforms will be advanced by the development of new methods for the fluorescence labeling of analytes and standard sizing ladders. Here we evaluate end-labeling of commercially available DNA ladders and polymerase chain reaction (PCR) amplicons with terminal deoxynucleotidyl transferase (TdT) as a method for fluorescent double-stranded DNA sizing analysis. A PCR-based procedure for the facile construction of custom energy-transfer-labeled DNA sizing ladders is also presented. High-resolution sizing of single-stranded DNA fragments is demonstrated with this energy-transfer-labeled ladder. These DNA labeling procedures will be useful for double-and single-stranded DNA analyses on microdevices and other electrophoretic platforms.

Base Sequence↗