Raman spectroscopic studies of the structures, energetics, and bond distortions of substrates bound to enzymes

Attenuated total reflection-Fourier transform infrared spectroscopy: a universal analytical technique with promising applications in forensic analyses

Contemporary criminal investigations are based on the statements made by the victim and the eyewitnesses. They also rely on the physical evidences found in the crime scene. These evidences, and more particularly biological ones, have a great judicial value in the courtroom. They are usually used to revoke the suspect's allegations and confirm or refute the statements made by the victim and the witnesses. Stains of body fluids are biological evidences highly sought by forensic investigators. In many criminal cases, the success of the investigation relies on the correct identification and classification of these stains. Therefore, the adoption of reliable and accurate forensic analytical methods seems to be of vital importance to attain this objective. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) is a modern and universal analytical technique capable of fingerprint recognition of the analyte using minimal amount of the test sample. The current systematic review aims to through light on the fundamentals of this technique and to illustrate its wide range of applications in forensic investigations. ATR-FTIR is a nondestructive technique which has demonstrated an exceptional efficiency in detecting, identifying and discriminating between stains of various types of body fluids usually encountered in crime scenes. The ATR-FTIR spectral data generated from bloodstains can be used to deduce a wealth of information related to the donor species, age, gender, and race. These data can also be exploited to discriminate between stains of different types of bloods including menstrual and peripheral bloods. In addition, ATR-FTIR has a great utility in the postmortem investigations. More particularly, in estimating the postmortem interval and diagnosing death caused by extreme weather conditions. It is also useful in diagnosing some ambiguous death causes such as fatal anaphylactic shock and diabetic ketoacidosis.

Molecular heterogeneities in the thermal expansivity of polyalcohols

Density is the key quantity for nearly all the numerous theories of the (dynamic) glass transition of supercooled liquids and melts. As mean field quantity, it is used to describe correlations and heterogeneities between regions consisting of several molecules. In contrast, the question how density is created by the interactions (i.e., bonds) within a molecule and to its nearest neighbors is almost unexplored. To investigate this for the example of a homologous series of polyalcohols (glycerol, threitol, xylitol, and sorbitol), Fourier-Transform InfraRed (FTIR) spectroscopy is carried out in a wide range of temperatures from far above to far below the calorimetric glass transition T_g. This enables us to determine the potentials and hence the bond lengths of specific intramolecular and intermolecular interactions. While the former has an expansion coefficient of (∼0.1 pm/100 K) with only smooth changes, the latter shows a 30-40 times stronger response with pronounced kinks at T_g. A comparison with the overall expansion based on mass density reveals that one has to separate between strong (OH⋅⋅⋅O) and weak (CH⋅⋅⋅O) intermolecular hydrogen (H)-bridges. Despite the fact that the latter dominates glassy dynamics, their expansivity is 5 times smaller than that of the weak H-bridges. It is to be expected that such heterogeneities on intramolecular and intermolecular scales are a general phenomenon in liquids and glassy systems demonstrating especially the necessity of atomistic simulations.

Correlations between the structure and the vibrational spectrum of the phosphate group. Implications for the analysis of an important functional group in phosphoproteins

Density functional theory calculations were used to establish correlations between the structure and the vibrational spectrum of the phosphate group in model compounds for phosphorylated amino acids. The model compounds were acetyl phosphate, methyl phosphate, and p-tolyl phosphate, which represented the phosphorylated amino acids aspartyl phosphate, serine or threonine phosphate, and tyrosine phosphate, respectively. The compounds were placed in different environments consisting of one or several HF or H₂O molecules, which modeled interactions of phosphorylated amino acids in the protein environment. The calculations were performed with the B3LYP functional and the 6-311++G(3df, 3pd) basis set. In general, the wavenumbers (or frequencies) of the stretching vibrations of the terminal P–O bonds correlated better with bond lengths of the phosphate group than with its bond angles. The best correlations were obtained with the shortest and the mean terminal P–O bond lengths with standard deviations from the trend line of only 0.2 pm. Other useful correlations were observed with the bond length difference between the shortest and longest terminal P–O bond and with the bond length of the bridging P–O bond.

Vibrational frequencies of phosphate are sensitive to bond length changes on the sub-picometer scale.

Interaction Enthalpy of Side Chain and Backbone Amides in Polyglutamine Solution Monomers and Fibrils

We determined an empirical correlation that relates the amide I vibrational band frequencies of the glutamine (Q) side chain to the strength of hydrogen bonding, van der Waals, and Lewis acid-base interactions of its primary amide carbonyl. We used this correlation to determine the Q side chain carbonyl interaction enthalpy (Δ H_int) in monomeric and amyloid-like fibril conformations of D₂Q₁₀K₂ (Q10). We independently verified these Δ H_int values through molecular dynamics simulations that showed excellent agreement with experiments. We found that side chain-side chain and side chain-peptide backbone interactions in fibrils and monomers are more enthalpically favorable than are Q side chain-water interactions. Q10 fibrils also showed a more favorable Δ H_int for side chain-side chain interactions compared to backbone-backbone interactions. This work experimentally demonstrates that interamide side chain interactions are important in the formation and stabilization of polyQ fibrils.

Tracking Reactive Water and Hydrogen-Bonding Networks in Photosynthetic Oxygen Evolution

In oxygenic photosynthesis, photosystem II (PSII) converts water to molecular oxygen through four photodriven oxidation events at a Mn₄CaO₅ cluster. A tyrosine, YZ (Y161 in the D1 polypeptide), transfers oxidizing equivalents from an oxidized, primary chlorophyll donor to the metal center. Calcium or its analogue, strontium, is required for activity. The Mn₄CaO₅ cluster and YZ are predicted to be hydrogen bonded in a water-containing network, which involves amide carbonyl groups, amino acid side chains, and water. This hydrogen-bonded network includes amino acid residues in intrinsic and extrinsic subunits. One of the extrinsic subunits, PsbO, is intrinsically disordered. This extensive (35 Å) network may be essential in facilitating proton release from substrate water. While it is known that some proteins employ internal water molecules to catalyze reactions, there are relatively few methods that can be used to study the role of water. In this Account, we review spectroscopic evidence from our group supporting the conclusion that the PSII hydrogen-bonding network is dynamic and that water in the network plays a direct role in catalysis. Two approaches, transient electron paramagnetic resonance (EPR) and reaction-induced FT-IR (RIFT-IR) spectroscopies, were used. The EPR experiments focused on the decay kinetics of YZ• via recombination at 190 K and the solvent isotope, pH, and calcium dependence of these kinetics. The RIFT-IR experiments focused on shifts in amide carbonyl frequencies, induced by photo-oxidation of the metal cluster, and on the isotope-based assignment of bands to internal, small protonated water clusters at 190, 263, and 283 K. To conduct these experiments, PSII was prepared in selected steps along the catalytic pathway, the S_n state cycle (n = 0-4). This cycle ultimately generates oxygen. In the EPR studies, S-state dependent changes were observed in the YZ• lifetime and in its solvent isotope effect. The YZ• lifetime depended on the presence of calcium at pH 7.5, but not at pH 6.0, suggesting a two-donor model for PCET. At pH 6.0 or 7.5, barium and ammonia both slowed the rate of YZ• recombination, consistent with disruption of the hydrogen-bonding network. In the RIFT-IR studies of the S state transitions, infrared bands associated with the transient protonation and deprotonation of internal waters were identified by D₂O and H₂¹⁸O labeling. The infrared bands of these protonated water clusters, W_n⁺ (or nH₂O(H₃O)⁺, n = 5-6), exhibited flash dependence and were produced during the S₁ to S₂ and S₃ to S₀ transitions. Calcium dependence was observed at pH 7.5, but not at pH 6.0. S-state induced shifts were observed in amide C═O frequencies during the S₁ to S₂ transition and attributed to alterations in hydrogen bonding, based on ammonia sensitivity. In addition, isotope editing of the extrinsic subunit, PsbO, established that amide vibrational bands of this lumenal subunit respond to the S state transitions and that PsbO is a structural template for the reaction center. Taken together, these spectroscopic results support the hypothesis that proton transfer networks, extending from YZ to PsbO, play a functional and dynamic role in photosynthetic oxygen evolution.

Conformational properties and aggregation of homo-oligomeric β3 (R)-valine peptides in organic solvents

The conformational characteristics of protected homo-oligomeric Boc-[β³ (R)Val]_n -OMe, n = 1, 2, 3, 4, 6, 9, and 12 have been investigated in organic solvents using nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) absorption spectroscopy and circular dichroism (CD) methods. The detailed ¹ H NMR analysis of Boc-[β³ (R)Val]₁₂ -OMe reveals that the peptide aggregates extensively in CDCl₃ , but is disaggregated in 20%, (v/v) dimethyl sulfoxide (DMSO) in CDCl₃ and in CD₃ OH. Limited assignment of the N-terminus NH groups, together with solvent dependence of NH chemical shifts and temperature coefficients provides evidence for 14-helix conformation in the 12-residue peptide. FTIR analysis in CHCl₃ establishes that the onset of folding and aggregation, as evidenced by NH stretching bands at 3375 cm^-1 (intramolecular) and 3285 cm^-1 (intermolecular), begins at the level of the tetrapeptide. The observed CD bands, 214 nm (negative) and 198 nm (positive), support 14-helix formation in the 9 and 12 residue sequences. The folding and aggregation tendencies of homo-oligomeric α-, β-, and γ- residues is compared in the model peptides Boc-[ωVal]_n -NHMe, ω = α, β, and γ and n = 1, 2, and 3. Analysis of the FTIR spectra in CHCl₃ , establish that the tendency to aggregate at the di and tripeptide level follows the order β > α∼γ, while the tendency to fold follows the order γ > β > α.

Exquisite Modulation of the Active Site of Methanocaldococcus jannaschii Adenylosuccinate Synthetase in Forward Reaction Complexes

In enzymes that conduct complex reactions involving several substrates and chemical transformations, the active site must reorganize at each step to complement the transition state of that chemical step. Adenylosuccinate synthetase (ADSS) utilizes a molecule each of guanosine 5'-monophosphate (GTP) and aspartate to convert inosine 5'-monophosphate (IMP) into succinyl adenosine 5'-monophosphate (sAMP) through several kinetic intermediates. Here we followed catalysis by ADSS through high-resolution vibrational spectral fingerprints of each substrate and intermediate involved in the forward reaction. Vibrational spectra show differential ligand distortion at each step of catalysis, and band positions of substrates are influenced by binding of cosubstrates. We found that the bound IMP is distorted toward its N1-deprotonated form even in the absence of any other ligands. Several specific interactions between GTP and active-site amino acid residues result in large Raman shifts and contribute substantially to intrinsic binding energy. When both IMP and GTP are simultaneously bound to ADSS, IMP is converted into an intermediate 6-phosphoryl inosine 5'-monophosphate (6-pIMP). The 6-pIMP·ADSS complex was found to be stable upon binding of the third ligand, hadacidin (HDA), an analogue of l-aspartate. We find that in the absence of HDA, 6-pIMP is quickly released from ADSS, is unstable in solution, and converts back into IMP. HDA allosterically stabilizes ADSS through local conformational rearrangements. We captured this complex and determined the spectra and structure of 6-pIMP in its enzyme-bound state. These results provide important insights into the exquisite tuning of active-site interactions with changing substrate at each kinetic step of catalysis.

Solution structure of ligands involved in purine salvage pathway

Analogues of intermediates involved in the purine salvage pathway can be exploited as potential drug molecules against enzymes of protozoan parasites. To develop such analogues we need knowledge of the solution structures, predominant tautomer at physiological pH and protonation-state of the corresponding natural ligand. In this regard, we have employed ultraviolet resonance Raman spectroscopy (UVRR) in combination with density functional theory (DFT) to study the solution structures of two relatively unexplored intermediates, 6-phosphoryl IMP (6-pIMP) and succinyl adenosine-5'-monophosphate (sAMP), of purine salvage pathway. These molecules are intermediates in a two step enzymatic process that converts inosine-5'-monpophosphate (IMP) to adenosine-5'-monophosphate (AMP). Experimental data on the molecular structure of these ligands is lacking. We report UVRR spectra of these two ligands, obtained at an excitation wavelength of 260 nm. Using isotope induced shifts and DFT calculations we assigned observed spectra to computed normal modes. We find that sAMP exists as neutral species at physiological pH and the predominant tautomer in solution bears proton at N10 position of purine ring. Though transient in solution, 6-pIMP is captured in the enzyme-bound form. This work provides the structural information of these ligands in solution state at physiological pH. We further compare these structures with the structures of AMP and IMP. Despite the presence of similar purine rings in AMP and sAMP, their UVRR spectra are found to be very different. Similarly, though the purine ring in 6-pIMP resembles that of IMP, UVRR spectra of the two molecules are distinct. These differences in the vibrational spectra provide direct information on the effects of exocyclic groups on the skeletal structures of these molecules. Our results identify key bands in the vibrational spectra of these ligands which may serve as markers of hydrogen bonding interactions upon binding to the active-sites of enzymes.

Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy

Raman spectroscopy is a form of vibrational spectroscopy based on inelastic scattering of light. In resonance Raman spectroscopy, the wavelength of the incident light falls within an absorption band of a chromophore, and this overlap of excitation and absorption energy greatly enhances the Raman scattering efficiency of the absorbing species. The ability to probe vibrational spectra of select chromophores within a complex mixture of molecules makes resonance Raman spectroscopy an excellent tool for studies of biomolecules. In this Current Topic, we discuss the type of molecular insights obtained from steady-state and time-resolved resonance Raman studies of a prototypical photoactive protein, rhodopsin. We also review recent efforts in ultraviolet resonance Raman investigations of soluble and membrane-associated biomolecules, including integral membrane proteins and antimicrobial peptides. These examples illustrate that resonance Raman is a sensitive, selective, and practical method for studying the structures of biological molecules, and the molecular bonding, geometry, and environments of protein cofactors, the backbone, and side chains.

Quantifying bond distortions in transient enzyme species by a combination of density functional theory calculations and time-resolved infrared difference spectroscopy. Implications for the mechanism of dephosphorylation of the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA1a)

The sarcoplasmic Ca(2+)-ATPase (SERCA1a) forms two phosphoenzyme intermediates during Ca(2+) pumping. The second intermediate E2P hydrolyzes rapidly, which is essential for the rapid removal of Ca(2+) from the cytosol of muscle cells. The present work studies whether a weakening of the scissile PO bond in the E2P ground state facilitates dephosphorylation. To this end, the experimentally known vibrational spectrum of the E2P phosphate group was calculated with density functional theory (DFT) using structural models at two levels of structural complexity: (i) Models of acetyl phosphate in simple environments and (ii) ~150 atom models of the catalytic site. It was found that the enzyme environment distorts the structure of the phosphate group: one of the terminal PO bonds is shorter in the catalytic site indicating weaker interactions than in water. However, the bond that bridges phosphate and Asp351 is unaffected. This indicates that the scissile PO bond is not weakened by the enzyme environment of E2P. A second finding was that the catalytic site of the E2P state in aqueous solution appears to adopt a structure as in the crystals with BeF3(-), where the ATPase is in a non-reactive conformation. The reactant state of the dephosphorylation reaction differs from the E2P ground state: Glu183 faces Asp351 and positions the attacking water molecule. This state has a 0.04Å longer, and thus weaker, bridging PO bond. The reactant state is not detected in our experiments, indicating that its energy is at least 1kcal/mol higher than that of the E2P ground state.

Calcium and the Hydrogen-Bonded Water Network in the Photosynthetic Oxygen-Evolving Complex

In photosynthesis, photosystem II evolves oxygen from water at a Mn4CaO5 cluster (OEC). Calcium is required for biological oxygen evolution. In the OEC, a water network, extending from the calcium to four peptide carbonyl groups, has recently been predicted by a high-resolution crystal structure. Here, we use carbonyl vibrational frequencies as reporters of electrostatic changes to test the presence of this water network. A single flash, oxidizing Mn(III) to Mn(IV) (the S1 to S2 transition), upshifted the frequencies of peptide C═O bands. The spectral change was attributable to a decrease in C═O hydrogen bonding. Strontium, which supports a lower level of steady state activity, also led to an oxidation-induced shift in C═O frequencies, but treatment with barium and magnesium, which do not support activity, did not. This work provides evidence that calcium maintains an electrostatically responsive water network in the OEC and shows that OEC peptide carbonyl groups can be used as solvatochromic markers.

Enzyme active site interactions by Raman/FTIR, NMR, and ab initio calculations

Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis.

Real-time Raman microspectroscopy scanning of the single live sperm bound to human zona pellucida

OBJECTIVE

To determine if Raman microspectroscopy (RMS) can distinguish sperm bound to the human zona pellucida (ZP) from those unbound sperm.

DESIGN

Paired experiments to compare Raman scanning features of ZP-bound and unbound sperm.

SETTING

Public hospital-based clinical assisted reproduction center.

PATIENT(S)

Sperm samples from ten fertile donors were used in this study.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Sperm-ZP binding, ZP-induced acrosome reaction, and scanning intensity of various regions of sperm.

RESULT(S)

The RMS found two slightly low-intensity regions (800-900 and 3,200-4,000 cm(-1)) shifted to high-intensity grade at the acrosome region of the ZP-bound sperm compared with unbound sperm. Moreover, principal component analysis and statistical analysis showed that the RMS can distinguish the ZP-bound sperm from the unbound sperm.

CONCLUSION(S)

RMS scanning of single live sperm could be used to distinguish ZP-bound sperm from unbound sperm. Thus, RMS may be a useful tool to detect normal functional sperm and to select sperm for intracytoplasmic sperm injection.

Fourier transform infrared (FTIR) spectroscopy

Fourier transform infrared (FTIR) spectroscopy probes the vibrational properties of amino acids and cofactors, which are sensitive to minute structural changes. The lack of specificity of this technique, on the one hand, permits us to probe directly the vibrational properties of almost all the cofactors, amino acid side chains, and of water molecules. On the other hand, we can use reaction-induced FTIR difference spectroscopy to select vibrations corresponding to single chemical groups involved in a specific reaction. Various strategies are used to identify the IR signatures of each residue of interest in the resulting reaction-induced FTIR difference spectra. (Specific) Isotope labeling, site-directed mutagenesis, hydrogen/deuterium exchange are often used to identify the chemical groups. Studies on model compounds and the increasing use of theoretical chemistry for normal modes calculations allow us to interpret the IR frequencies in terms of specific structural characteristics of the chemical group or molecule of interest. This review presents basics of FTIR spectroscopy technique and provides specific important structural and functional information obtained from the analysis of the data from the photosystems, using this method.

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.

RAMAN CRYSTALLOGRAPHY AND OTHER BIOCHEMICAL APPLICATIONS OF RAMAN MICROSCOPY

Recent studies using a Raman microscope have shown that single protein crystals provide an ideal platform to undertake Raman difference spectroscopic analyses under nonresonance conditions. This approach, termed Raman crystallography, provides a means of characterizing chemical events within the crystal such as ligand binding and enzyme reactions. In many cases Raman crystallography goes hand in hand with X-ray crystallographic studies because the Raman results can inform the X-ray crystallographer about the status of chemical events in the crystal prior to flash freezing and X-ray analysis. In turn, the combined data from the Raman and X-ray analyses are highly synergistic and offer novel perspectives on structure and dynamics in enzyme active sites. In a related area, protein misfolding, Raman microscopy can provide detailed insights into the chemistry of the amyloid plaques associated with Alzheimer's disease and into the intermediates on the alpha-synuclein protein misfolding pathway implicated in Parkinson's disease.

Quantifying energetic contributions to ground state destabilization

Vibrational spectroscopy has identified that in many cases, substrate association with enzyme active sites results in significant bond polarization. This bond polarization can be attributed to a combination of desolvation, conformational restriction, and true polarization by the local electric field. Quantum chemical calculations permit the extent of polarization to be quantified both in terms of partial charge and energy. The changes in vibrational frequency that occur during the binding process necessarily result in equilibrium isotope effects. The equilibrium isotope effect on association is one feature that differentiates isotope effects on k(cat) and k(cat)/K(m). An improved chemical understanding of the changes that occur on substrate binding will help elucidate the role of substrate activation in enzyme catalysis.

Mapping interactions between the Ca2+-ATPase and its substrate ATP with infrared spectroscopy

Infrared spectroscopy has been used to map substrate-protein interactions: the conformational changes of the sarcoplasmic reticulum Ca(2+)-ATPase upon nucleotide binding and ATPase phosphorylation were monitored using the substrate ATP and ATP analogues (2'-deoxy-ATP, 3'-deoxy-ATP, and inosine 5'-triphosphate), which were modified at specific functional groups of the substrate. Modifications to the 2'-OH, the 3'-OH, and the amino group of adenine reduce the extent of binding-induced conformational change of the ATPase, with particularly strong effects observed for the latter two. This demonstrates the structural sensitivity of the nucleotide-ATPase complex to individual interactions between nucleotide and ATPase. All groups studied are important for binding and interactions of a given ligand group with the ATPase depend on interactions of other ligand groups. Phosphorylation of the ATPase was observed for ITP and 2'-deoxy-ATP, but not for 3'-deoxy-ATP. There is no direct link between the extent of conformational change upon nucleotide binding and the rate of phosphorylation showing that the full extent of the ATP-induced conformational change is not mandatory for phosphorylation. As observed for the nucleotide-ATPase complex, the conformation of the first phosphorylated ATPase intermediate E1PCa(2) also depends on the nucleotide, indicating that ATPase states have a less uniform conformation than previously anticipated.

Stereoselectivity of enoyl-CoA hydratase results from preferential activation of one of two bound substrate conformers

Enoyl-CoA hydratase catalyzes the hydration of trans-2-crotonyl-CoA to 3(S)- and 3(R)-hydroxybutyryl-CoA with a stereoselectivity (3(S)/3(R)) of 400,000 to 1. Importantly, Raman spectroscopy reveals that both the s-cis and s-trans conformers of the substrate analog hexadienoyl-CoA are bound to the enzyme, but that only the s-cis conformer is polarized. This selective polarization is an example of ground state strain, indicating the existence of catalytically relevant ground state destabilization arising from the selective complementarity of the enzyme toward the transition state rather than the ground state. Consequently, the stereoselectivity of the enzyme-catalyzed reaction results from the selective activation of one of two bound substrate conformers rather than from selective binding of a single conformer. These findings have important implications for inhibitor design and the role of ground state interactions in enzyme catalysis.