Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

Phase-sensitive detection in modulation excitation spectroscopy applied to potential induced electron transfer in cytochrome c oxidase

Cytochrome c oxidase (CcO) from Rhodobacter sphaeroides was investigated by modulated excitation surface-enhanced infrared-absorption spectroscopy (SEIRAS). Sequential electron transfer (ET) within CcO was initiated by electrochemical excitation. During modulated excitation by periodic potential pulses with frequencies between 20 and 500 Hz, time-resolved infrared spectra were measured by the step-scan technique, with time resolution in the millisecond range. Conformational changes of the protein structure as a result of ET lead to rather complex SEIRA spectra with many overlapping bands embedded in a broad background signal. Phase-sensitive detection (PSD) was used to separate single components within the broad band of overlapping structural bands in the amide I region. PSD is able to extract the periodic response of single components with the same frequency as the excitation from noise or from static background and therefore enhances the signal-to-noise ratio. Moreover, PSD enables validation of the fit model used for the deconvolution of overlapping bands by analyzing phase lags of single components acquired at different stimulation frequencies. Phase lags between the evaluated vibrational components and the modulated excitation increase with increasing excitation frequencies, an inherent prerequisite of this evaluation method.

Honey bee odorant-binding protein 14: effects on thermal stability upon odorant binding revealed by FT-IR spectroscopy and CD measurements

In the present work, we study the effect of odorant binding on the thermal stability of honey bee (Apis mellifera L.) odorant-binding protein 14. Thermal denaturation of the protein in the absence and presence of different odorant molecules was monitored by Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD). FT-IR spectra show characteristic bands for intermolecular aggregation through the formation of intermolecular β-sheets during the heating process. Transition temperatures in the FT-IR spectra were evaluated using moving-window 2D correlation maps and confirmed by CD measurements. The obtained results reveal an increase of the denaturation temperature of the protein when bound to an odorant molecule. We could also discriminate between high- and low-affinity odorants by determining transition temperatures, as demonstrated independently by the two applied methodologies. The increased thermal stability in the presence of ligands is attributed to a stabilizing effect of non-covalent interactions between odorant-binding protein 14 and the odorant molecule.

Characterization of large amyloid fibers and tapes with Fourier transform infrared (FT-IR) and Raman spectroscopy

Amyloids are self-assembled protein structures implicated in a host of neurodegenerative diseases. Organisms can also produce "functional amyloids" to perpetuate life, and these materials serve as models for robust biomaterials. Amyloids are typically studied using fluorescent dyes, Fourier transform infrared (FT-IR), or Raman spectroscopy analysis of the protein amide I region, and X-ray diffraction (XRD) because the self-assembled β-sheet secondary structure of the amyloid can be easily identified with these techniques. Here, FT-IR and Raman spectroscopy analyses are described to characterize amyloid structures beyond just identification of the β-sheet structure. It has been shown that peptide mixtures can self-assemble into nanometer-sized amyloid structures that then continue to self-assemble to the micrometer scale. The resulting structures are flat tapes of low rigidity or cylinders of high rigidity depending on the peptides in the mixture. By monitoring the aggregation of peptides in solution using FT-IR spectroscopy, it is possible to identify specific amino acids implicated in β-sheet formation and higher order self-assembly. It is also possible to predict the final tape or cylinder morphology and gain insight into the structure's physical properties based on observed intermolecular interactions during the self-assembly process. Tapes and cylinders are shown to both have a similar core self-assembled β-sheet structure. Soft tapes also have weak hydrophobic interactions between alanine, isoleucine, leucine, and valine that facilitate self-assembly. Rigid cylinders have similar hydrophobic interactions that facilitate self-assembly and also have extensive hydrogen bonding between glutamines. Raman spectroscopy performed on the dried tapes and fibers shows the persistence of these interactions. The spectroscopic analyses described could be generalized to other self-assembling amyloid systems to explain property and morphological differences.

Reversible chirality control in peptide-functionalized gold nanoparticles

We report the induction of chiroptical properties in 2 nm diameter gold nanoparticles passivated with short peptides characterized by the Aib-l-Ala repetition in their sequence. The nanoparticles present relevant ECD signals in the 300-650 nm wavelength region, corresponding to the gold nanoparticle's quantized electronic structure. Although the only chiral amino acid present in the peptide sequences is l-Ala, the particles show mirror image spectra like those of enantiomers according to the number of amino acids in the main chain (odd or even). Such a behavior appears to be strongly influenced by the secondary structure assumed by the peptides when passivating the nanoparticles and vanishes when the sequence is long enough to assume a 310-helix conformation. Moreover, chirality control is a reversible process and can be deactivated or reactivated by increasing or decreasing the temperature.

Over-expression and characterization of NS3 and NS5A of Hepatitis C virus genotype 3a

Background

Hepatitis C virus (HCV) is a common and leading cause for liver cirrhosis and hepatocellular carcinoma. Current therapies to treat HCV infection are shown to be partially effective and poorly tolerated. Therefore, ample efforts are underway to rationally design therapies targeting the HCV non-structural proteins. Most of the work carried out in this direction has been focusing mainly on HCV genotype 1. Two direct-acting antiviral agents (DAAs) Telaprevir and Boceprevir are being used against genotype 1a infection in combination therapy with interferon and ribavirin. Unfortunately these DAAs are not effective against genotype 3a. Considering the wide spread infection by HCV genotype 3a in developing countries especially South Asia, we have focused on the recombinant production of antiviral drug targets NS3 and NS5A from HCV genotype 3a. These protein targets are to be used for screening of inhibitors.

Results

High-level expression of NS3 and NS5A was achieved at 25°C, using ~1 and 0.5 mM Isopropyl β-D-1-thiogalactopyranoside (IPTG), respectively. Yields of the purified NS3 and NS5A were 4 and 1 mg per liter culture volume, respectively. Although similar amounts of purified NS3 were obtained at 25 and 14°C, specificity constant (K_cat/K_m) was somewhat higher at expression temperature of 25°C. Circular dichroism (CD) and Fourier-transform infrared (FT-IR) spectroscopy revealed that both NS3 and NS5A contain a mixture of alpha-helix and beta-sheet secondary structures. For NS3 protein, percentages of secondary structures were similar to the values predicted from homology modeling.

Conclusions

NS3 and NS5A were over-expressed and using Nickel-affinity method both proteins were purified to ~ 95% purity. Yield of the purified NS3 obtained is four fold higher than previous reports. CD spectroscopy revealed that difference in activity of NS3 expressed at various temperatures is not related to changes in global structural features of the protein. Moreover, CD and FT-IR analysis showed that NS3 and NS5A contain both alpha-helical and beta-sheet structures and for NS5A, the proportion is almost equal. The production of NS3 and NS5A in milligram quantities will allow their characterization by biophysical and biochemical means that will help in designing new strategies to fight against HCV infection.

High-resolution sizing of monolayer-protected gold clusters by differential centrifugal sedimentation

Differential centrifugal sedimentation (DCS) has been applied to accurately size ligand-protected gold hydrosols in the 10 to 50 nm range. A simple protocol is presented to correct for particle density variations due to the presence of the ligand shell, which is formed here by either polyethylene glycol-substituted alkane thiols (PEG-alkane thiols) of different chain length or oligopeptides. The method gives reliable data for all particle sizes investigated and lends itself to rapid routine sizing of nanoparticles. Unlike TEM, DCS is highly sensitive to small changes in the thickness of the organic ligand shell and can be applied to monitor shell thickness variations of as little as 0.1 nm on particles of a given core size.

Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics

As it remains practically impossible to generate ergodic ensembles for large intrinsically disordered proteins (IDP) with molecular dynamics (MD) simulations, it becomes critical to compare spectroscopic characteristics of the theoretically generated ensembles to corresponding measurements. We develop a Bayesian framework to infer the ensemble properties of an IDP using a combination of conformations generated by MD simulations and its measured infrared spectrum. We performed 100 different MD simulations totaling more than 10 µs to characterize the conformational ensemble of αsynuclein, a prototypical IDP, in water. These conformations are clustered based on solvent accessibility and helical content. We compute the amide-I band for these clusters and predict the thermodynamic weights of each cluster given the measured amide-I band. Bayesian analysis produces a reproducible and non-redundant set of thermodynamic weights for each cluster, which can then be used to calculate the ensemble properties. In a rigorous validation, these weights reproduce measured chemical shifts.

Iodothyronine-phospholipid interactions in the lipid gel phase probed by Raman spectral markers

A better understanding of the structural effects induced by thyroid hormones in model membranes is attained by Raman spectroscopy. The interactions of T3 and T4 with multilamellar vesicles of dipalmytoylphosphatidylcholine (DPPC) in the gel phase are characterized by analyzing the spectral behavior of the C-H and C-C stretching vibrations of the acyl chains. The spectra evidence an increase in the relative number of gauche conformation, which indicates the hormones are able to penetrate into the hydrophobic region of the bilayer and partially alter the lipid structure. In addition, the density packing of the acyl chains appears increased and the rotational mobility of the terminal methylene groups is slightly reduced in the iodothyronine/DPPC mixtures. These effects are interpreted in terms of the transition to an interdigitated phase due to the hormone incorporation to the membrane. The polar heads of the lipids also interact with the hormone, as evidenced by the PO2(-) symmetric stretching band.

Coordination structures of Mg2+ and Ca2+ in three types of tobacco calmodulins in solution: Fourier-transform infrared spectroscopic studies of side-chain COO- groups

Calmodulin (CaM) is a Ca(2+)-binding protein that regulates a number of fundamental cellular activities. Nicotiana tabacum CaM (NtCaM) comprises 13 genes classified into three types, among which gene expression and target enzyme activation differ. We performed Fourier-transform infrared spectroscopy to compare the secondary and coordination structures of Mg(2+) and Ca(2+) among NtCaM1, NtCaM3, and NtCaM13 as representatives of the three types of NtCaMs. Data suggested that NtCaM13 has a different secondary structure due to the weak β-strand bands and the weak 1661 cm(-1) band. Coordination structures of Mg(2+) of NtCaM3 and NtCaM13 were similar but different from that of NtCaM1, while the Ca(2+)-binding manner was similar among the three CaMs. The amplitude differences of the band at 1554-1550 cm(-1) obtained by second-derivative spectra indicated that the intensity change of the band of NtCaM13 was smaller in response to [Ca(2+)] increases under low [Ca(2+)] conditions than were those of NtCaM1 and NtCaM3, while the intensity reached the same level under high [Ca(2+)]. Therefore, NtCaM13 has a characteristic secondary structure and specific Mg(2+)-binding manner and needs higher [Ca(2+)] for bidentate Ca(2+) coordination of 12th Glu in EF-hand motifs. The Ca(2+)-binding mechanisms of the EF-hand motifs of the three CaMs are similar; however, the cation-dependent conformational change in NtCaM13 is unique among the three NtCaMs.

Heterologous expression, characterization and evaluation of the matrix protein from Newcastle disease virus as a target for antiviral therapies

Newcastle disease virus (NDV) is an infectious agent of a large variety of birds, including chicken, which poses a real threat to the agriculture industry. Matrix (M) proteins of NDV and many other viruses perform critical functions during viral assembly and budding from the host cell. M-proteins are well conserved and therefore are potential targets for antiviral therapies. To validate this, we expressed the NDV M-protein in its native form in Saccharomyces cerevisiae and in inclusion bodies in Escherichia coli. Proper refolding of the recombinant protein produced in E. coli was verified using circular dichroism and infrared spectroscopies and electron microscopy. Immunization of chickens with the NDV M-protein elicited significant serum antibody titers. However, the antibodies conferred little protection against the ND following lethal viral challenges. We conclude that the M-protein is not exposed on the surface of the host cell or the virus at any stage during its life cycle. We discuss how the conserved M-protein can further be exploited as an antiviral drug target.

Physicochemical characterization of the staphylolytic LysK enzyme in complexes with polycationic polymers as a potent antimicrobial

Staphylococcus aureus causes many serious visceral, skin, and respiratory diseases. About 90% of its clinical strains are multi-drug resistant, but the use of bacteriophage lytic enzymes offers a viable alternative to antibiotic therapy. LysK, the phage K endolysin, can lyse S. aureus when purified and exposed externally. It has been investigated in its complexes with polycationic polymers (poly-l-lysines (PLLs) of molecular weights 2.5, 9.6, and 55.2 kDa and their block copolymers with polyethylene glycol PLL10-PEG114, PLL30-PEG114, and PLL30-PEG23) as a basis for creating active and stable antimicrobial. Complexing with polycationic PLLs produces a stabilizing effect on LysK due to structure ordering in its molecules and break-down of aggregates as a result of electrostatic interaction. The stability of LysK in the presence of PLL-PEG block copolymers improves by both electrostatic and hydrophobic mechanisms. Complexes of LysK with 2.5, 9.6, 55.2 kDa poly-l-lysines and PLL30-PEG114 have demonstrated sufficient stability at the temperatures of physiological activity (37 °C) and storage (4 °C and 22 °C).

Characterization of casein hydrolysates derived from enzymatic hydrolysis

Background

Casein is the main proteinaceous component of milk and has made us interest due to its wide applications in the food, drug, and cosmetic industries as well as to its importance as an investigation material for elucidating essential questions regarding the protein chemistry. Enzymatic hydrolysis is an important method commonly used in the modification of protein structure in order to enhance the functional properties of proteins. The relationship between enzymatic hydrolysis and structure change of casein need to make more study.

Results

During hydrolysis, degree of hydrolysis in the casein hydrolysates increased rapidly in the initial 20 minutes, reached a plateau after 45 minutes, and then kept relative constant for the rest of the hydrolysis. The relative percentage of the released peptides with molecular weight of over 50 kD significantly decreased with hydrolyzation, while those with MW of 30–50 kD and below 20 kD increased significantly. The contents of a-helix and β-turn in the hydrolysates increased compared to the original casein. Moreover, the molecular flexibilities of the casein hydrolysates, estimated by the ratio of α-helix to β-structure, were lower than that of original casein protein.

Conclusions

The significant changes in molecular weight distribution and structure characteristics of casein hydrolysates were found compared to the control sample. This change should be the basis of enhancement of functional properties.

Graphene oxide-induced conformation changes of glucose oxidase studied by infrared spectroscopy

The adsorption of proteins on the surface of nanomaterials can induce changes in the structure and biological activity of the proteins. Although there have been a number of studies aimed at developing an understanding of the interactions of proteins with surfaces of nanomaterials, a detailed description of the actual state of the adsorbed proteins or the functional consequences of protein adsorption onto nanomaterials has yet to be reported. In this study, the conformation changes of glucose oxidase (GOx) induced by adsorption on graphene oxide (GO) sheets were investigated by quantitative second-derivative infrared analysis and two-dimensional infrared correlation spectroscopy (2D IR). The adsorption of GOx on GO sheets resulted in the conversion of α-helix to β-sheet structures and therefore led to substantial conformation changes of GOx, even the unfolding of the protein. These alterations in the conformation of GOx caused a significant decrease in the catalytic activity of the enzyme for glucose oxidation. This study demonstrates that nanomaterials can strongly influence the conformation and activity of adsorbed proteins. In addition to the importance of this effect in cases of the direct adsorption of proteins on nanomaterials, the results have implications for proteins adsorbed on materials with nanometer-scale surface roughness.

Relative stability of human centrins and its relationship to calcium binding

Centrins are calcium binding proteins that belong to the EF-hand superfamily with diverse biological functions. Herein we present the first systematic study that establishes the relative stability of related centrins via complementary biophysical techniques. Our results define the stepwise molecular behavior of human centrins by two-dimensional infrared (2D IR) correlation spectroscopy, the change in heat capacity and enthalpy of denaturation by differential scanning calorimetry, and the relative stability of the helical regions of centrins by circular dichroism. More importantly, 2D IR correlation spectroscopy provides unique information about the similarities and differences in dynamics between these related proteins. The thermally induced molecular behavior of human centrins can be used to predict biological target interactions that have a relative dependence on calcium affinity. This information is essential for understanding why certain isoforms may be used to rescue a phenotype and therefore also for explaining the different functions these proteins may have in vivo. Furthermore, this comparative approach can be applied to the study of recombinant therapeutic protein candidates for the treatment of disease states.

FTIR spectroscopic imaging of protein aggregation in living cells

Protein misfolding and aggregation are the hallmark of a number of diseases including Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and the prion diseases. In all cases, a naturally-occurring protein misfolds and forms aggregates that are thought to disrupt cell function through a wide range of mechanisms that are yet to be fully unraveled. Fourier transform infrared (FTIR) spectroscopy is a technique that is sensitive to the secondary structure of proteins and has been widely used to investigate the process of misfolding and aggregate formation. This review focuses on how FTIR spectroscopy and spectroscopic microscopy are being used to evaluate the structural changes in disease-related proteins both in vitro and directly within cells and tissues. Finally, ongoing technological advances will be presented that are enabling time-resolved FTIR imaging of protein aggregation directly within living cells, which can provide insight into the structural intermediates, time scale, and mechanisms of cell toxicity associated with aggregate formation. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.

The interconversion between a flexible β-sheet and a fibril β-arrangement constitutes the main conformational event during misfolding of PSD95-PDZ3 domain

The temperature-induced misfolding pathway of PDZ3, the third PDZ domain of the PSD95 neuronal protein, is populated by a trimeric β-sheet-rich intermediate state that leads to a stepwise and reversible formation of supramacromolecular structures. Using FTIR, we have found that misfolding of this pathway is not due to different ensembles of a variety of precursors, but comes mainly from the interconversion of a flexible β-sheet of the domain to wormlike fibrils. The appearance of the wormlike fibril FTIR component is also accompanied by a slight decrease of the band that corresponds to loops in the native state, whereas the rest of the regular elements of secondary structure are fairly well maintained upon misfolding. Transmission electron microscope micrographs have confirmed the presence of wormlike fibrils upon heating at 60°C, where the trimeric intermediate is maximally populated. Toxicity assays in the human neuroblastoma cell line SH-SY5Y show that cytotoxicity increases as the aggregation pathway proceeds. NMR analysis of chemical shifts as a function of temperature has revealed, as one of the main conformational aspects of such an interconversion at the residue level, that the β-sheet arrangement around strand β3 promotes the change that drives misfolding of the PDZ3 domain.

Binding of β-amyloid (1-42) peptide to negatively charged phospholipid membranes in the liquid-ordered state: modeling and experimental studies

To explore the initial stages of amyloid β peptide (Aβ42) deposition on membranes, we have studied the interaction of Aβ42 in the monomeric form with lipid monolayers and with bilayers in either the liquid-disordered or the liquid-ordered (L(o)) state, containing negatively charged phospholipids. Molecular dynamics (MD) simulations of the system have been performed, as well as experimental measurements. For bilayers in the L(o) state, in the absence of the negatively charged lipids, interaction is weak and it cannot be detected by isothermal calorimetry. However, in the presence of phosphatidic acid, or of cardiolipin, interaction is detected by different methods and in all cases interaction is strongest with lower (2.5-5 mol%) than higher (10-20 mol%) proportions of negatively charged phospholipids. Liquid-disordered bilayers consistently allowed a higher Aβ42 binding than L(o) ones. Thioflavin T assays and infrared spectroscopy confirmed a higher proportion of β-sheet formation under conditions when higher peptide binding was measured. The experimental results were supported by MD simulations. We used 100 ns MD to examine interactions between Aβ42 and three different 512 lipid bilayers consisting of palmitoylsphingomyelin, dimyristoyl phosphatidic acid, and cholesterol in three different proportions. MD pictures are different for the low- and high-charge bilayers, in the former case the peptide is bound through many contact points to the bilayer, whereas for the bilayer containing 20 mol% anionic phospholipid only a small fragment of the peptide appears to be bound. The MD results indicate that the binding and fibril formation on the membrane surface depends on the composition of the bilayer, and is the result of a subtle balance of many inter- and intramolecular interactions between the Aβ42 and membrane.

Characterization of recombinant antibodies for cancer therapy by infrared spectroscopy

Fourier transform infrared (FTIR) spectroscopy was used to study the structure of the recombinant antibodies 1E10, anti-CD20 and hR3, which are used as anti-cancer therapeutic drugs. We tested their sensitivity against different conditions and treatments such as pH, temperature, freeze-thaw cycles and drying, which are relevant for the practical usefulness of the drugs. All antibodies were stable against moderate temperature increases (up to 50 °C) and pH changes (range 5-9). 1E10 was sensitive to extreme pH values (pH 3 and 12), whereas hR3 was most sensitive to temperature (at and above 60 °C). We did not observe any significant changes upon freeze-thaw and drying treatments. The secondary structure content of all three antibodies was estimated to be similar to that of IgG with ∼64% β-sheet, 0% α-helix and ∼36% other structure.

Covalent α-synuclein dimers: chemico-physical and aggregation properties

The aggregation of α-synuclein into amyloid fibrils constitutes a key step in the onset of Parkinson's disease. Amyloid fibrils of α-synuclein are the major component of Lewy bodies, histological hallmarks of the disease. Little is known about the mechanism of aggregation of α-synuclein. During this process, α-synuclein forms transient intermediates that are considered to be toxic species. The dimerization of α-synuclein could represent a rate-limiting step in the aggregation of the protein. Here, we analyzed four covalent dimers of α-synuclein, obtained by covalent link of the N-terms, C-terms, tandem cloning of two sequences and tandem juxtaposition in one protein of the 1–104 and 29–140 sequences. Their biophysical properties in solution were determined by CD, FT-IR and NMR spectroscopies. SDS-induced folding was also studied. The fibrils formation was analyzed by ThT and polarization fluorescence assays. Their morphology was investigated by TEM and AFM-based quantitative morphometric analysis. All dimers were found to be devoid of ordered secondary structure under physiological conditions and undergo α-helical transition upon interaction with SDS. All protein species are able to form amyloid-like fibrils. The reciprocal orientation of the α-synuclein monomers in the dimeric constructs affects the kinetics of the aggregation process and a scale of relative amyloidogenic propensity was determined. Structural investigations by FT IR spectroscopy, and proteolytic mapping of the fibril core did not evidence remarkable difference among the species, whereas morphological analyses showed that fibrils formed by dimers display a lower and diversified level of organization in comparison with α-synuclein fibrils. This study demonstrates that although α-synuclein dimerization does not imply the acquisition of a preferred conformation by the participating monomers, it can strongly affect the aggregation properties of the molecules. The results presented highlight a substantial role of the relative orientation of the individual monomer in the definition of the fibril higher structural levels.

Coordination to divalent cations by calcium-binding proteins studied by FTIR spectroscopy

We review the Fourier-transform infrared (FTIR) spectroscopy of side-chain COO(-) groups of Ca(2+)-binding proteins: parvalbumins, bovine calmodulin, akazara scallop troponin C and related calcium binding proteins and peptide analogues. The COO(-) stretching vibration modes can be used to identify the coordination modes of COO(-) groups of Ca(2+)-binding proteins to metal ions: bidentate, unidentate, and pseudo-bridging. FTIR spectroscopy demonstrates that the coordination structure of Mg(2+) is distinctly different from that of Ca(2+) in the Ca(2+)-binding site in solution. The interpretation of COO(-) stretches is ensured on the basis of the spectra of calcium-binding peptide analogues. The implication of COO(-) stretches is discussed for Ca(2+)-binding proteins. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.

Molecular basis for membrane pore formation by Bax protein carboxyl terminus

Bax protein plays a key role in mitochondrial membrane permeabilization and cytochrome c release upon apoptosis. Our recent data have indicated that the 20-residue C-terminal peptide of Bax (BaxC-KK; VTIFVAGVLTASLTIWKKMG), when expressed intracellularly, translocates to the mitochondria and exerts lethal effect on cancer cells. Moreover, the BaxC-KK peptide, as well as two mutants where the two lysines are replaced with glutamate (BaxC-EE) or leucine (BaxC-LL), have been shown to form relatively large pores in lipid membranes, composed of up to eight peptide molecules per pore. Here the pore structure is analyzed by polarized Fourier transform infrared, circular dichroism, and fluorescence experiments on the peptides reconstituted in phospholipid membranes. The peptides assume an α/β-type secondary structure within membranes. Both β-strands and α-helices are significantly (by 30-60 deg) tilted relative to the membrane normal. The tryptophan residue embeds into zwitterionic membranes at 8-9 Å from the membrane center. The membrane anionic charge causes a deeper insertion of tryptophan for BaxC-KK and BaxC-LL but not for BaxC-EE. Combined with the pore stoichiometry determined earlier, these structural constraints allow construction of a model of the pore where eight peptide molecules form an "α/β-ring" structure within the membrane. These results identify a strong membranotropic activity of Bax C-terminus and propose a new mechanism by which peptides can efficiently perforate cell membranes. Knowledge on the pore forming mechanism of the peptide may facilitate development of peptide-based therapies to kill cancer or other detrimental cells such as bacteria or fungi.

Correlation between catalytic activity and secondary structure of subtilisin dissolved in organic solvents

Fourier-transform infrared (FTIR) spectroscopy has been used to quantify the alpha-helix and beta-sheet contents of subtilisin Carlsberg dissolved in several nonaqueous, as well as aqueous, solvents. Independently, the catalytic activity of the enzyme has been measured in the same solvents. While our previous FTIR studies revealed no connection between the secondary structure and enzymatic activity for subtilisin suspended in various organic solvents, a very different situation is observed herein for the dissolved enzyme. Specifically, if either the alpha-helix or beta-sheet content in a given solvent is higher or lower than in water, no appreciable enzymatic catalysis is observed. Conversely, when the secondary structure of subtilisin dissolved in a given nonaqueous solvent is similar to that in water, so is the enzymatic activity. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 485-491, 1997.

Self-assembly of amphipathic β-sheet peptides: insights and applications

Amphipathic peptides composed of alternating polar and nonpolar residues have a strong tendency to self-assemble into one-dimensional, amyloid-like fibril structures. Fibrils derived from peptides of general (XZXZ)(n) sequence in which X is hydrophobic and Z is hydrophilic adopt a putative β-sheet bilayer. The bilayer configuration allows burial of the hydrophobic X side chain groups in the core of the fibril and leaves the polar Z side chains exposed to solvent. This architectural arrangement provides fibrils that maintain high solubility in water and has facilitated the recent exploitation of self-assembled amphipathic peptide fibrils as functional biomaterials. This article is a critical review of the development and application of self-assembling amphipathic peptides with a focus on the fundamental insight these types of peptides provide into peptide self-assembly phenomena.

Synthesis of silica particles and their application as supports for alcohol dehydrogenases and cofactor immobilizations: conformational changes that lead to switch in enzyme stereoselectivity

FTIR, circular dichroism (CD) and fluorescence spectroscopies were used to characterize conformational changes in horse liver alcohol dehydrogenase (HLADH) and ketoreductase (KRED 117) upon physical and covalent immobilizations on silica particles (functionalized with amino, epoxy and thiol groups) of different sizes. Conformational changes for immobilized enzymes were associated with high and low frequency shifts of the amide I and II bands. CD spectra of native HLADH and KRED 117 characterized with a negative peak at 222nm indicating a α-helical structure. The disappearance of the negative peak in the CD spectra of immobilized enzymes and appearance of a positive peak at 222nm supported these observations. These findings demonstrated unfolding of folded enzymes and exposure of the amino acid residues during denaturation with a red shift in tryptophan fluorescence. The decrease in specific activities (by 60-70% in all cases) for both immobilized enzymes was correlated to those of conformational changes. Silica-attached enzyme-NADH systems were evaluated for enantioselective reduction of 1-(p-methoxyphenyl)-propan-2-one. Conformational changes enhanced the enantioselectivity of immobilized HLADH with a switch in its stereoselectivity. In the case of immobilized KRED 117, kinetic values (V(max) and K(m)) were lower than that of the free enzyme, without enhancing enzyme enantio- and stereoselectivity.

Amyloid-derived peptide forms self-assembled monolayers on gold nanoparticle with a curvature-dependent β-sheet structure

Using a combination of Fourier transform infrared (FTIR) spectroscopy and solid-state nuclear magnetic resonance (SSNMR) techniques, the secondary structure of peptides anchored on gold nanoparticles of different sizes is investigated. The structure of the well-studied CALNN-capped nanoparticles is compared to the structure of nanoparticles capped with a new cysteine-terminated peptide, CFGAILSS. The design of that peptide is derived from the minimal amyloidogenic sequence FGAIL of the human islet polypeptide amylin. We demonstrate that CFGAILSS forms extended fibrils in solution. When constrained at a nanoparticle surface, CFGAILSS adopts a secondary structure markedly different from CALNN. Taking into account the surface selection rules, the FTIR spectra of CFGAILSS-capped gold nanoparticles indicate the formation of β-sheets which are more prominent for 25 nm diameter nanoparticles than for 5 nm nanoparticles. No intermolecular (13)C-(13)C dipolar coupling is detected with rotational resonance SSNMR for CALNN-capped nanoparticles, while CALNN is in a random coil configuration. Coupling is detected for CFGAILSS-capped gold nanoparticles, however, consistent with an intermolecular (13)C-(13)C distance of 5.0 ± 0.3 Å, in agreement with intermolecular hydrogen bonding in a parallel β-sheet structure.

Fourier transform infrared spectroscopy of intrinsically disordered proteins: measurement procedures and data analyses

A peculiar property of intrinsically disordered proteins (IDPs), or of intrinsically disordered domains, is the absence of a well-defined three dimensional structure under native conditions. Moreover, IDPs usually acquire a specific structure in the presence of different interactors. In this framework, Fourier transform infrared (FTIR) spectroscopy is a powerful tool to assess the disordered character of a protein and to study its induced folding. In this chapter, we will show the detailed experimental procedures to measure the FTIR spectra of protein samples and the spectral analyses required to obtain information on the protein secondary structures and aggregation.