Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy

On the recombination of hydronium and hydroxide ions in water

The recombination of hydronium and hydroxide ions following water ionization is one of the most fundamental processes determining the pH of water. The neutralization step once the solvated ions are in close proximity is phenomenologically understood to be fast, but the molecular mechanism has not been directly probed by experiments. We elucidate the mechanism of recombination in liquid water with ab initio molecular dynamics simulations, and it emerges as quite different from the conventional view of the Grotthuss mechanism. The neutralization event involves a collective compression of the water-wire bridging the ions, which occurs in approximately 0.5 ps, triggering a concerted triple jump of the protons. This process leaves the neutralized hydroxide in a hypercoordinated state, with the implications that enhanced collective compressions of several water molecules around similarly hypercoordinated states are likely to serve as nucleation events for the autoionization of liquid water.

Preparation of a family of 10-hydroxybenzo[h]quinoline analogues via a modified Sanford reaction and their excited state intramolecular proton transfer properties

We have developed a highly optimized methodology that allows for the oxidative acetoxylation of a sterically and electronically demanding library of analogues of benzo[h]quinoline. The optimal conditions for the insertion of an OAc group were identified after examining various reaction parameters (solvent, oxidant, catalyst, temperature, time). The conditions identified (Pd(OAc)(2), PhI(OAc)(2), MeCN, 150 °C, 16 h), combined with the hydrolysis of acetates, resulted in the formation of hydroxybenzoquinolines in 27-59% yield, whereas all previously published procedures were ineffective. This synthesis was compatible with diverse functionalities (ester, aldehyde, carbon-carbon triple bond) and, most importantly, worked for sterically hindered analogues as well as for compounds possessing electron-donating and electron-withdrawing substituents at various positions. All the obtained compounds demonstrated excited-state intramolecular proton transfer (ESIPT) manifesting as small fluorescence quantum yields and large Stokes shifts (8300-9660 cm(-1)). The effect of structural variations in eight 10-hydroxybenzo[h]quinoline analogues on absorption and emission properties was studied in detail.

6-Hydroxyindole-based borondipyrromethene: synthesis and spectroscopic studies

A 6-hydroxyindole-based BODIPY, named BODIPY-OH, with distinct spectroscopic characteristics is reported. Through a systematic study of the spectroscopic characteristics of BODIPY-OH and BODIPY-O(-) in various solvents containing an organic base, we found that the light-color of the fluorophore can be tuned over a wide range by changing the polarity of solvent/base combinations. The absorption color of the solution can be tuned over a range of 100 nm and the emission color within a wide range from 571 to 681 nm by simply converting the phenol form of BODIPY-OH to the phenolate form. Fluorescence of BODIPY-O(-) with high quantum yield shows relatively large Stokes shift in solvent/base combinations, which are ascribed to the excited state deprotonation from (BODIPY-OH)* to (BODIPY-O(-))*, followed by emission from the ion form.

Fine tuning the energetics of excited-state intramolecular proton transfer (ESIPT): white light generation in a single ESIPT system

Using 7-hydroxy-1-indanone as a prototype (I), which exhibits excited-state intramolecular proton transfer (ESIPT), chemical modification has been performed at C(2)-C(3) positions by fusing benzene (molecule II) and naphthalene rings, (molecule III). I undergoes an ultrafast rate of ESIPT, resulting in a unique tautomer emission (λ(max) ∼530 nm), whereas excited-state equilibrium is established for both II and III, as supported by the dual emission and the associated relaxation dynamics. The forward ESIPT (normal to proton-transfer tautomer species) rates for II and III are deduced to be (30 ps)(-1) and (22 ps)(-1), respectively, while the backward ESIPT rates are (11 ps)(-1) and (48 ps)(-1). The ESIPT equilibrium constants are thus calculated to be 0.37 and 2.2 for II and III, respectively, giving a corresponding free energy change of 0.59 and -0.47 kcal/mol between normal and tautomer species. For III, normal and tautomer emissions in solid are maximized at 435 and 580 nm, respectively, achieving a white light generation with Commission Internationale de l'Eclairage (CIE) (0.30, 0.27). An organic light-emitting diode based on III is also successfully fabricated with maximum brightness of 665 cd m(-2) at 20 V (885 mA cm(-2)) and the CIE coordinates of (0.26, 0.35). The results provide the proof of concept that the white light generation can be achieved in a single ESIPT system.

Excited-state intramolecular proton transfer molecules bearing o-hydroxy analogues of green fluorescent protein chromophore

o-Hydroxy analogues, 1a-g, of the green fluorescent protein chromophore have been synthesized. Their structures and electronic properties were investigated by X-ray single-crystal analyses, electrochemistry, and luminescence properties. In solid and nonpolar solvents 1a-g exist mainly as Z conformers that possess a seven-membered-ring hydrogen bond and undergo excited-state intramolecular proton transfer (ESIPT) reactions, resulting in a proton-transfer tautomer emission. Fluorescence upconversion dynamics have revealed a coherent type of ESIPT, followed by a fast vibrational/solvent relaxation (<1 ps) to a twisted (regarding exo-C(5)-C(4)-C(3) bonds) conformation, from which a fast population decay of a few to several tens of picoseconds was resolved in cyclohexane. Accordingly, the proton-transfer tautomer emission intensity is moderate (0.08 in 1e) to weak (∼10(-4) in 1a) in cyclohexane. The stronger intramolecular hydrogen bonding in 1g suppresses the rotation of the aryl-alkene bond, resulting in a high yield of tautomer emission (Φ(f) ≈ 0.2). In the solid state, due to the inhibition of exo-C(5)-C(4)-C(3) rotation, intense tautomer emission with a quantum yield of 0.1-0.9 was obtained for 1a-g. Depending on the electronic donor or acceptor strength of the substituent in either the HOMO or LUMO site, a broad tuning range of the emission from 560 (1g) to 670 nm (1a) has been achieved.

Proton transfer events in GFP

Proton transfer is one of the most important elementary processes in biology. Green fluorescent protein (GFP) serves as an important model system to elucidate the mechanistic details of this reaction, because in GFP proton transfer can be induced by light absorption. Illumination initiates proton transfer through a 'proton-wire', formed by the chromophore (the proton donor), water molecule W22, Ser205 and Glu222 (the acceptor), on a picosecond time scale. To obtain a more refined view of this process, we have used a combined approach of time resolved mid-infrared spectroscopy and visible pump-dump-probe spectroscopy to resolve with atomic resolution how and how fast protons move through this wire. Our results indicate that absorption of light by GFP induces in 3 ps (10 ps in D(2)O) a shift of the equilibrium positions of all protons in the H-bonded network, leading to a partial protonation of Glu222 and to a so-called low barrier hydrogen bond (LBHB) for the chromophore's proton, giving rise to dual emission at 475 and 508 nm. This state is followed by a repositioning of the protons on the wire in 10 ps (80 ps in D(2)O), ultimately forming the fully deprotonated chromophore and protonated Glu222.

Impact of carbondiimide crosslinker used for magnetic carbon nanotube mediated GFP plasmid delivery

1-Ethyl-3-(3-dimethylaminopropyl) carbondiimide hydrochloride (EDC) is commonly used as a crosslinker to help bind biomolecules, such as DNA plasmids, with nanostructures. However, EDC often remains, after a crosslink reaction, in the micro-aperture of the nanostructure, e.g., carbon nanotube. The remaining EDC shows positive green fluorescent signals and makes a nanostructure with a strong cytotoxicity which induces cell death. The toxicity of EDC was confirmed on a breast cancer cell line (MCF-7) and two leukemic cell lines (THP-1 and KG-1). The MCF-7 cells mainly underwent necrosis after treatment with EDC, which was verified by fluorescein isothiocyanate (FITC) annexin V staining, video microscopy and scanning electronic microscopy (SEM). If the EDC was not removed completely, the nanostructures with remaining EDC produced a green fluorescent background that could interfere with flow cytometry (FACS) measurement and result in false information about GFP plasmid delivery. Effective methods to remove residual EDC on macromolecules were also developed.

Surface-Enhanced Femtosecond Stimulated Raman Spectroscopy

Surface-enhanced Raman spectroscopy (SERS) and femtosecond stimulated Raman spectroscopy (FSRS) have revolutionized the Raman spectroscopy field. SERS provides spectroscopic detection of single molecules, and FSRS enables the acquisition of Raman spectra on the ultrafast time scale of molecular motion. Here, we present the first successful combination of these two techniques, demonstrating surface-enhanced femtosecond stimulated Raman spectroscopy (SE-FSRS) using gold nanoantennas with embedded reporter molecules. Using a picosecond Raman and femtosecond probe pulse, the time- and ensemble-averaged enhancement factor is estimated to be in the range of 10(4)-10(6). We report the line shapes, power dependence, and magnitude of the SE-FSRS signal and discuss contributions to sample degradation on the minute time scale. With these first successful proof-of-principle experiments, time-resolved SE-FSRS techniques can now be rationally attempted with the goals of investigating the dynamics of plasmonic materials as well as examining the contributions of environmental heterogeneities by probing more homogeneous molecular subsets.

Quantum theory of time-resolved femtosecond stimulated Raman spectroscopy: direct versus cascade processes and application to CDCl3

We present a quantum mechanical wave packet treatment of time-resolved femtosecond stimulated Raman spectroscopy (FSRS), or two-dimensional (2D) FSRS, where a vibrational coherence is initiated with an impulsive Raman pump which is subsequently probed by FSRS. It complements the recent classical treatment by Mehlenbacher et al. [J. Chem. Phys. 131, 244512 (2009)]. In this 2D-FSRS, two processes can occur concurrently but with different intensities: a direct fifth-order process taking place on one molecule, and a cascade process comprising two third-order processes on two different molecules. The cascade process comprises a parallel and a sequential cascade. The theory is applied to the 2D-FSRS of CDCl(3) where calculations showed that: (a) the cascade process is stronger than the direct fifth-order process by one order of magnitude, (b) the sidebands assigned to C-Cl E and A(1) bends, observed on both sides of the Stokes C-D stretch frequency, are not due to anharmonic coupling between the C-D stretch and the C-Cl bends, but are instead due to the coherent anti-Stokes Raman spectroscopy (CARS) and coherent Stokes Raman spectroscopy (CSRS) fields produced in the first step of the cascade process, (c) for each delay time between the femtosecond impulsive pump and FSRS probe pulses, the line shape of the sidebands shows an inversion symmetry about the C-D stretch frequency, and this is due to the 180(∘) phase difference between the CARS and CSRS fields that produced the left and right sidebands, and (d) for each sideband, the line shape changes from positive Lorentzian to dispersive to negative Lorentzian, then to negative dispersive and back to positive Lorentzian with the period of the bending vibration, and it is correlated with the momentum of the wave packet prepared on the ground-state surface by the impulsive pump along the sideband normal coordinate.

Stabilizing role of glutamic acid 222 in the structure of Enhanced Green Fluorescent Protein

Enhanced Green Fluorescent Protein (EGFP) is a variant of wild-type Green Fluorescent Protein from the jellyfish Aequorea victoria, whose mutations S65T and F64L increase brightness and folding efficiency. EGFP is extensively used in cell biology and biochemistry as a colocalization or expression reporter. Surprisingly, the structure of this very popular protein has not been determined yet. We report here its crystallographic structure at 1.5Å resolution which shows significant differences in the vicinity of residue 64 and of the chromophore. In particular, two conformations are observed for the key residue glutamic acid 222, in apparent contradiction with the single fluorescence lifetime of the protein. We then show that X-ray induced decarboxylation of Glu222 during diffraction data collection results in the disruption of a hydrogen-bond network near the chromophore. Using single-crystal microspectrophotometry, we demonstrate that this correlates with a significant loss of the fluorescence properties. We thus propose a mechanism of bleaching of the protein at low temperature. Taken together, these two sets of results highlight the stabilizing role of Glu222 to the chromophore cavity of EGFP.

Function and structure of GFP-like proteins in the protein data bank

The RCSB protein databank contains 266 crystal structures of green fluorescent proteins (GFP) and GFP-like proteins. This is the first systematic analysis of all the GFP-like structures in the pdb. We have used the pdb to examine the function of fluorescent proteins (FP) in nature, aspects of excited state proton transfer (ESPT) in FPs, deformation from planarity of the chromophore and chromophore maturation. The conclusions reached in this review are that (1) The lid residues are highly conserved, particularly those on the "top" of the β-barrel. They are important to the function of GFP-like proteins, perhaps in protecting the chromophore or in β-barrel formation. (2) The primary/ancestral function of GFP-like proteins may well be to aid in light induced electron transfer. (3) The structural prerequisites for light activated proton pumps exist in many structures and it's possible that like bioluminescence, proton pumps are secondary functions of GFP-like proteins. (4) In most GFP-like proteins the protein matrix exerts a significant strain on planar chromophores forcing most GFP-like proteins to adopt non-planar chromophores. These chromophoric deviations from planarity play an important role in determining the fluorescence quantum yield. (5) The chemospatial characteristics of the chromophore cavity determine the isomerization state of the chromophore. The cavities of highlighter proteins that can undergo cis/trans isomerization have chemospatial properties that are common to both cis and trans GFP-like proteins.

Femtosecond stimulated Raman spectrometer in the 320-520nm range

Multi-µJ narrow-bandwidth (≈ 10 cm(-1)) picosecond pulses, broadly tunable in the visible-UV range (320-520 nm), are generated by spectral compression of femtosecond pulses emitted by an amplified Ti:sapphire system. Such pulses provide the ideal Raman pump for broadband femtosecond stimulated Raman spectroscopy, as here demonstrated on a heme protein.

Coherent nonlinear optical imaging: beyond fluorescence microscopy

The quest for ultrahigh detection sensitivity with spectroscopic contrasts other than fluorescence has led to various novel approaches to optical microscopy of biological systems. Coherent nonlinear optical imaging, especially the recently developed nonlinear dissipation microscopy (including stimulated Raman scattering and two-photon absorption) and pump-probe microscopy (including excited-state absorption, stimulated emission, and ground-state depletion), provides new image contrasts for nonfluorescent species. Thanks to the high-frequency modulation transfer scheme, these imaging techniques exhibit superb detection sensitivity. By directly interrogating vibrational and/or electronic energy levels of molecules, they offer high molecular specificity. Here we review the underlying principles and excitation and detection schemes, as well as exemplary biomedical applications of this emerging class of molecular imaging techniques.

1,8,1',8'-Tetrakis(dimethylamino)-2,2'-dinaphthylmethanols: double in/out proton sponges with low-barrier hydrogen-bond switching

Previously unknown bis[1,8-bis(dimethylamino)naphth-2-yl]phenylmethanol (5) and bis[1,8-bis(dimethylamino)naphth-2-yl]methanol (6) have been obtained and studied by combination of X-ray, NMR, and IR techniques at variable temperature. It has been established that both proton sponge units in the solid tertiary alcohol 5 exist in nonconventional in/out form, one of which is fixed by intramolecular O-H...N hydrogen bonding. In solution, a fast interconversion of two isoenergetic hydrogen chelates occurs which can be frozen below 183 K. Unlike this, the secondary alcohol 6 in the solid at 100 K adopts the in/out-in/in conformation and at 293 K demonstrates a kind of dynamic behavior which can be described as temperature-driven dimer-induced rechelation. In solution under ambient conditions 6 exists as an equilibrating mixture of chelated and unchelated monomeric forms in a approximately 1:1.8 molar ratio.

Spectral-structural effects of the keto-enol-enolate and phenol-phenolate equilibria of oxyluciferin

The effects of environmental polarity on the enolization of the keto form and the deprotonation of the enol, and the role of the neutral and ionized 6'-OH group in the fluorescence of the firefly emitter, oxyluciferin, were assessed through a detailed study of the structure and absorption and fluorescence spectra of its 6'-dehydroxylated analogue. It was found that the deprotonated 6'-O(-) group is a necessary, albeit insufficient, factor in accounting for the observed yellow-green and red emissions of oxyluciferin. Its negative charge is essential for effective excited-state charge transfer, which lowers the emission energy and broadens the emission spectrum. Deprotonation of the 6'-OH group changes its effect on the emission energy from blue- to red-shifting. Furthermore, the combination of these opposite effects and resonance stabilization of the phenolate-keto form causes switching of the order of maximum emission wavelengths of the three species involved in the keto-enol-enolate equilibrium from enol << keto < enolate in absence of 6'-OH to keto < enol << enolate with 6'-OH, to enol < enolate < keto with 6'-O(-). If only the keto-enol-enolate equilibrium is considered, solvents of medium polarity are the most effective in decreasing the excited-state energy. Polar or very polar environments also stimulate shift of the ground-state equilibrium toward the enol form. Under such circumstances, the enol group can be partly or completely deprotonated in the ground state or from the excited state: a polar environment facilitates the ionization, while a less polar environment requires the presence of a stronger base. In the absence of bases, the ground-state keto form exists only in solvents of very weak to medium polarity, but with stronger bases, it can also exist in a nonpolar or very weakly polar environment, usually together with the enolate anion. The phenol-enolate form of oxyluciferin, a species that could not be experimentally detected prior to this study, was identified as a yellow-emitting species.

ULTRA: A Unique Instrument for Time-Resolved Spectroscopy

We report the development of a high-sensitivity time-resolved infrared and Raman spectrometer with exceptional experimental flexibility based on a 10-kHz synchronized dual-arm femtosecond and picosecond laser system. Ultrafast high-average-power titanium sapphire lasers and optical parametric amplifiers provide wavelength tuning from the ultraviolet (UV) to the mid-infrared region. Customized silicon, indium gallium arsenide, and mercury cadmium telluride linear array detectors are provided to monitor the probe laser intensity in the UV to mid-infrared wavelength range capable of measuring changes in sample absorbance of ΔOD ~ 10(-5) in 1 second. The system performance is demonstrated for the time-resolved infrared, two-dimensional (2D) infrared, and femtosecond stimulated Raman spectroscopy techniques with organometallic intermediates, organic excited states, and the dynamics of the tertiary structure of DNA.

On the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins

Tsien et al. (Science, 2009, 324, 804-807) recently reported the creation of the first infrared fluorescent protein (IFP). It was engineered from bacterial phytochrome by removing the PHY and histidine kinase-related domains, by optimizing the protein to prevent dimerization, and by limiting the biliverdins conformational freedom, especially around its D ring. We have used database analyses and molecular dynamics simulations with freely rotating chromophoric dihedrals in order to model the dihedral freedom available to the biliverdin D ring in the excited state and to show that the tetrapyrrole ligands in phytochromes are flexible and can adopt many conformations; however, their conformational space is limited/defined by the chemospatial characteristics of the protein cavity. Our simulations confirm that the reduced accessibility to conformations geared to an excited state proton transfer may be responsible for the fluorescence in IFP, just as has been suggested by Kennis et al. (Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 9170-9175) for fluorescent bacteriophytochrome from Rhodopseudomonas palustris.

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework

Energy landscape theories have provided a common ground for understanding the protein folding problem, which once seemed to be overwhelmingly complicated. At the same time, the native state was found to be an ensemble of interconverting states with frustration playing a more important role compared to the folding problem. The landscape of the folded protein – the native landscape – is glassier than the folding landscape; hence, a general description analogous to the folding theories is difficult to achieve. On the other hand, the native basin phase volume is much smaller, allowing a protein to fully sample its native energy landscape on the biological timescales. Current computational resources may also be used to perform this sampling for smaller proteins, to build a ‘topographical map’ of the native landscape that can be used for subsequent analysis. Several major approaches to representing this topographical map are highlighted in this review, including the construction of kinetic networks, hierarchical trees and free energy surfaces with subsequent structural and kinetic analyses. In this review, we extensively discuss the important question of choosing proper collective coordinates characterizing functional motions. In many cases, the substates on the native energy landscape, which represent different functional states, can be used to obtain variables that are well suited for building free energy surfaces and analyzing the protein's functional dynamics. Normal mode analysis can provide such variables in cases where functional motions are dictated by the molecule's architecture. Principal component analysis is a more expensive way of inferring the essential variables from the protein's motions, one that requires a long molecular dynamics simulation. Finally, the two popular models for the allosteric switching mechanism, ‘preexisting equilibrium’ and ‘induced fit’, are interpreted within the energy landscape paradigm as extreme points of a continuum of transition mechanisms. Some experimental evidence illustrating each of these two models, as well as intermediate mechanisms, is presented and discussed.

Topochemistry and photomechanical effects in crystals of green fluorescent protein-like chromophores: effects of hydrogen bonding and crystal packing

To obtain insight into the effects of the environment on the photophysics and photochemistry of the green fluorescence protein (GFP), eight crystal structures of six synthetic aryl-substituted analogues (2-fluoro, 2-methyl, 3-hydroxy, 3-methoxy, 2,4-dimethyl and 2,5-dimethyl) of the GFP chromophore (4-hydroxy-benzylidenedimethylimidazolinone) were determined and correlated with their two-dimensional steady-state and time-resolved solid-state excitation-emission spectra. The stacking between the molecules greatly affected the emission energy and the lifetime of the emission of the chromophore, implying that pi-pi interactions could be critical for the photophysics of GFP. The reaction pathways were dependent on the excitation energy, resulting either in [2 + 2] photodimerization at the bridging double bond (UV excitation) or flipping of the imidazolone ring (visible excitation). The meta-hydroxy chromophore (3-HOBDI) was the only GFP-chromophore analogue that was obtained as more than one stable polymorph in the pure state thus far. Due to the asymmetric substitution with hydrogen bond donors and acceptors, 3-HOBDI is tetramorphic, the forms showing distinctly different structure and behavior: (1) while one of the polymorphs (3-HOBDI-A), having multilayer structure with alternating stereochemistry of linear hydrogen-bonded motifs, undergoes photodimerization under UV light, (2) another (3-HOBDI-C), which has dimeric head-to-tail structure, shows Z-to-E isomerization via tau-one-bond flip of the imidazolone ring by excitation in the visible region. X-ray diffraction analysis of a partially reacted single crystal of 3-HOBDI-C provided the first direct evidence of tau-one-bond flip occurring in a GFP-like compound. Moreover, the cooperative action of the photodimerization of 3-HOBDI-A appears as a photomechanical effect of unprecedented magnitude for a single crystalline specimen, where photoexcited single crystals bend to more than 90 degrees without breaking.

Raman-assisted crystallography of biomolecules at the synchrotron: instrumentation, methods and applications

Raman spectroscopy is a powerful technique that, in recent years, has been successfully coupled to X-ray crystallography for the analysis of biological macromolecular systems. The complementarity between both techniques is illustrated at multiple stages, including sample preparation, data collection and structural interpretation with a mechanistic perspective. The current state of instrumentation is described, focusing on synchrotron based setups. Present and future applications of Raman microspectrophotometry are reviewed with reference to recent examples dealing with metallo-, photosensitive-, and redox-proteins. The added value of Raman microspectrophotometry to assess X-radiation damage is discussed, and its applicability to investigate crystalline DNA molecules is also emphasized. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome

Phytochromes are red-light photoreceptor proteins that regulate a variety of responses and cellular processes in plants, bacteria, and fungi. The phytochrome light activation mechanism involves isomerization around the C15 horizontal lineC16 double bond of an open-chain tetrapyrrole chromophore, resulting in a flip of its D-ring. In an important new development, bacteriophytochrome (Bph) has been engineered for use as a fluorescent marker in mammalian tissues. Here we report that an unusual Bph, RpBphP3 from Rhodopseudomonas palustris, denoted P3, is fluorescent. This Bph modulates synthesis of light-harvesting complex in combination with a second Bph exhibiting classical photochemistry, RpBphP2, denoted P2. We identify the factors that determine the fluorescence and isomerization quantum yields through the application of ultrafast spectroscopy to wild-type and mutants of P2 and P3. The excited-state lifetime of the biliverdin chromophore in P3 was significantly longer at 330-500 ps than in P2 and other classical phytochromes and accompanied by a significantly reduced isomerization quantum yield. H/D exchange reduces the rate of decay from the excited state of biliverdin by a factor of 1.4 and increases the isomerization quantum yield. Comparison of the properties of the P2 and P3 variants shows that the quantum yields of fluorescence and isomerization are determined by excited-state deprotonation of biliverdin at the pyrrole rings, in competition with hydrogen-bond rupture between the D-ring and the apoprotein. This work provides a basis for structure-based conversion of Bph into an efficient near-IR fluorescent marker.

The genome-wide association study--a new era for common polygenic disorders

This review covers the advances made in the last decade utilizing the high-density single-nucleotide microarrays to screen the entire human genome for genetic risk variants and outlines future strategies to draw deeper into the human genetic front. The sequence of the human genome provides the blueprint for life, while its variation provides the spice of life. Approximately 99.5% of the human genome DNA sequence is identical among humans with 0.5% of the genome sequence (15 million bps) accounting for all individual differences including susceptibility for disease. The new technology of the computerized chip array containing up to millions of SNPs as DNA markers makes possible genome-wide association studies to detect genetic predisposition to common polygenic disorders such as coronary artery disease (CAD). The sample sizes required for these studies are massive and large; worldwide consortiums such as CARDIoGRAM have been formed to accommodate this requirement. The progress has been remarkable with the identification of 9p21 followed by several others within the past 2 years. It is expected that most of the common variants (minor allele frequency, MAF >5%) will be identified for CAD within the next 2 to 3 years. Rare variants (MAF <5%) will require direct sequencing which will be delayed somewhat. The ultimate objective for the future is the sequencing and functional analysis of the causative polymorphisms. This will require a new approach involving several disciplines, namely, bioinformatics, high-throughput cell expression, and animal models.

Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle

We present the results of a systematic series of constrained minimum energy pathway calculations on ground state potential energy surfaces, for a cluster model of the proton chain transfer that mediates the photocycle of the green fluorescent protein, as well as for a model including the solvated protein environment. The calculations vary in terms of the types of modes that are assumed to be capable of relaxing in concert with the movement of the protons and the results demonstrate that the nature and extent of dynamical relaxation has a substantive impact on the activation energy for the proton transfer. We discuss the implications of this in terms of currently available dynamical models and chemical rate theories that might be brought to bear on the kinetics of this important example of proton chain transfer in a biological system.