4-Methoxypicolinic Acid N-Oxide: One of the Shortest Hydrogen Bonds Known Characterized by Neutron Diffraction, Inelastic Neutron Scattering, Infrared Spectroscopy, and Periodic DFT Calculations.

The present work focuses on the case of an extremely short intramolecular O-H···O hydrogen bond (H-bond) found in 4-methoxypicolinic acid N-oxide (MPANO). The donor···acceptor separation of 2.403 Å makes the H-bond in MPANO one of the shortest H-bonds known. We elucidated the structure and dynamics of the H-bond by two neutron-based techniques, namely, single-crystal diffraction and inelastic scattering (INS) vibrational spectroscopy. We also utilized conventional infrared (IR) spectroscopy as well as quantum chemical computations on isolated and periodic models. Both the protiated and deuterated variants of MPANO were investigated by INS and IR. All the methods used unequivocally confirm the existence of an extremely short, asymmetric H-bond, with the proton located near yet off the midpoint. The main relevant feature of the IR spectrum is an extremely broad, complex, and red-shifted OH (OD) stretching band spanning between 1800 and 500 cm-1 and centered at about 1360 cm-1, which indicates the presence of extensive anharmonicity and coupling with other H-bond modes. Of the modes characteristic of H-bond dynamics, only the out-of-plane OH (OD) bending can clearly be detected in the INS spectra; it has a relatively high frequency indicative of the strength of the H-bond. The computed structure is in excellent agreement with the diffraction measurement when periodicity is taken into account. The calculated harmonic frequencies show a reasonable match with the observed spectral features, whereby the assignment of the IR and INS spectra is facilitated. The hydrogen stretching frequency, however, appears to be significantly overestimated, on account of the limitations of the harmonic approximation and the complex nature of the short H-bond.

Toxicity of nitrophenolic pollutant 4-nitroguaiacol to terrestrial plants and comparison with its non-nitro analogue guaiacol (2-methoxyphenol).

Phenols, and especially their nitrated analogues, are ubiquitous pollutants and known carcinogens which have already been linked to forest decline. Although nitrophenols have been widely recognized as harmful to different aquatic and terrestrial organisms, we could not find any literature assessing their toxicity to terrestrial plants. Maize (monocot) and sunflower (dicot) were exposed to phenolic pollutants, guaiacol (GUA) and 4-nitroguaiacol (4NG), through a hydroponics system under controlled conditions in a growth chamber. Their acute physiological response was studied during a two-week root exposure to different concentrations of xenobiotics (0.1, 1.0, and 10 mM). The exposure visibly affected plant growth and the effect increased with increasing xenobiotic concentration. In general, 4NG affected plants more than GUA. Moreover, sunflower exhibited an adaptive response, especially to low and moderate GUA concentrations. The integrity of both plant species deteriorated during the exposure: biomass and photochemical pigment content were significantly reduced, which reflected in the poorer photochemical efficiency of photosystem II. Our results imply that 4NG is taken up by sunflower plants, where it could enter a lignin biosynthesis pathway.

Amyloid Formation of Stefin B Protein Studied by Infrared Spectroscopy.

BACKGROUND: Stefin B, an established model protein for studying the stability and mechanism of protein folding, was used for monitoring protein aggregation and formation of amyloid structure by infrared spectroscopy. METHODS: The analyses of the integral intensities of the low frequency part of the Amide I band, which is directly connected to the appearance of the cross-ß structure reveals the temperature but not pH dependence of stefin B structure. RESULTS: We show that pH value has significant role in the monomer stability of stefin B. Protein is less stable in acidic environment and becomes more stable in neutral or basic conditions. While in the case of the Amide I band area analysis we apply only spectral regions characteristic for only part of the protein in cross-ß structure, the temperature study using multivariate curve resolution (MCR) analysis contains also information about the protein conformation states which do not correspond to native protein nor protein in cross-ß structure. CONCLUSIONS: These facts results in the slightly different shapes of fitted sigmoid functions fitted to the weighted amount of the second basic spectrum (sc2), which is the closed approximation of the protein spectra with cross-ß structure. Nevertheless, the applied method detects the initial change of the protein structure. Upon the analysis of infrared data a model for stefin B aggregation is proposed.

Distinct conformational changes occur within the intrinsically unstructured pro-domain of pro-Nerve Growth Factor in the presence of ATP and Mg2.

Nerve growth factor (NGF), the prototypical neurotrophic factor, is involved in the maintenance and growth of specific neuronal populations, whereas its precursor, proNGF, is involved in neuronal apoptosis. Binding of NGF or proNGF to TrkA, p75NTR , and VP10p receptors triggers complex intracellular signaling pathways that can be modulated by endogenous small-molecule ligands. Here, we show by isothermal titration calorimetry and NMR that ATP binds to the intrinsically disordered pro-peptide of proNGF with a micromolar dissociation constant. We demonstrate that Mg2+ , known to play a physiological role in neurons, modulates the ATP/proNGF interaction. An integrative structural biophysics analysis by small angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry unveils that ATP binding induces a conformational rearrangement of the flexible pro-peptide domain of proNGF. This suggests that ATP may act as an allosteric modulator of the overall proNGF conformation, whose likely distinct biological activity may ultimately affect its physiological homeostasis.

Exploration of macromolecular phenotype of human skeletal muscle in diabetes using infrared spectroscopy.

Introduction: The global burden of diabetes mellitus is escalating, and more efficient investigative strategies are needed for a deeper understanding of underlying pathophysiological mechanisms. The crucial role of skeletal muscle in carbohydrate and lipid metabolism makes it one of the most susceptible tissues to diabetes-related metabolic disorders. In tissue studies, conventional histochemical methods have several technical limitations and have been shown to inadequately characterise the biomolecular phenotype of skeletal muscle to provide a holistic view of the pathologically altered proportions of macromolecular constituents. Materials and methods: In this pilot study, we examined the composition of five different human skeletal muscles from male donors diagnosed with type 2 diabetes and non-diabetic controls. We analysed the lipid, glycogen, and collagen content in the muscles in a traditional manner with histochemical assays using different staining techniques. This served as a reference for comparison with the unconventional analysis of tissue composition using Fourier-transform infrared spectroscopy as an alternative methodological approach. Results: A thorough chemometric post-processing of the infrared spectra using a multi-stage spectral decomposition allowed the simultaneous identification of various compositional details from a vibrational spectrum measured in a single experiment. We obtained multifaceted information about the proportions of the different macromolecular constituents of skeletal muscle, which even allowed us to distinguish protein constituents with different structural properties. The most important methodological steps for a comprehensive insight into muscle composition have thus been set and parameters identified that can be used for the comparison between healthy and diabetic muscles. Conclusion: We have established a methodological framework based on vibrational spectroscopy for the detailed macromolecular analysis of human skeletal muscle that can effectively complement or may even serve as an alternative to histochemical assays. As this is a pilot study with relatively small sample sets, we remain cautious at this stage in drawing definitive conclusions about diabetes-related changes in skeletal muscle composition. However, the main focus and contribution of our work has been to provide an alternative, simple and efficient approach for this purpose. We are confident that we have achieved this goal and have brought our methodology to a level from which it can be successfully transferred to a large-scale study that allows the effects of diabetes on skeletal muscle composition and the interrelationships between the macromolecular tissue alterations due to diabetes to be investigated.

Application of FTIR Spectroscopy to Detect Changes in Skeletal Muscle Composition Due to Obesity with Insulin Resistance and STZ-Induced Diabetes.

Age, obesity, and diabetes mellitus are pathophysiologically interconnected factors that significantly contribute to the global burden of non-communicable diseases. These metabolic conditions are associated with impaired insulin function, which disrupts the metabolism of carbohydrates, lipids, and proteins and can lead to structural and functional changes in skeletal muscle. Therefore, the alterations in the macromolecular composition of skeletal muscle may provide an indication of the underlying mechanisms of insulin-related disorders. The aim of this study was to investigate the potential of Fourier transform infrared (FTIR) spectroscopy to reveal the changes in macromolecular composition in weight-bearing and non-weight-bearing muscles of old, obese, insulin-resistant, and young streptozotocin (STZ)-induced diabetic mice. The efficiency of FTIR spectroscopy was evaluated by comparison with the results of gold-standard histochemical techniques. The differences in biomolecular phenotypes and the alterations in muscle composition in relation to their functional properties observed from FTIR spectra suggest that FTIR spectroscopy can detect most of the changes observed in muscle tissue by histochemical analyses and more. Therefore, it could be used as an effective alternative because it allows for the complete characterization of macromolecular composition in a single, relatively simple experiment, avoiding some obvious drawbacks of histochemical methods.

Untangling the Conformational Plasticity of V66M Human proBDNF Polymorphism as a Modifier of Psychiatric Disorder Susceptibility.

The human genetic variant BDNF (V66M) represents the first example of neurotrophin family member that has been linked to psychiatric disorders. In order to elucidate structural differences that account for the effects in cognitive function, this hproBDNF polymorph was expressed, refolded, purified, and compared directly to the WT variant for the first time for differences in their 3D structures by DSF, limited proteolysis, FT-IR, and SAXS measurements in solution. Our complementary studies revealed a deep impact of V66M polymorphism on hproBDNF conformations in solution. Although the mean conformation in solution appears to be more compact in the V66M variant, overall, we demonstrated a large increase in flexibility in solution upon V66M mutation. Thus, considering that plasticity in IDR is crucial for protein function, the observed alterations may be related to the functional alterations in hproBDNF binding to its receptors p75NTR, sortilin, HAP1, and SorCS2. These effects can provoke altered intracellular neuronal trafficking and/or affect proBDNF physiological functions, leading to many brain-associated diseases and conditions such as cognitive impairment and anxiety. The structural alterations highlighted in the present study may pave the way to the development of drug discovery strategies to provide greater therapeutic responses and of novel pharmacologic strategy in human populations with this common polymorphism, ultimately guiding personalized medicine for neuropsychiatric disorders.

Strong Hydrogen Bonds in Acetylenedicarboxylic Acid Dihydrate.

Acetylenedicarboxylic acid dihydrate (ADAD) represents a complex with strong hydrogen bonding between the carboxylic OH and the water molecule. An X-ray re-examination of the ADAD crystal structure confirms the O…O distance of the short hydrogen bonds, and clearly shows different bond lengths between the two oxygen atoms with respect to the carbon atom in the carboxyl group, indicating a neutral structure for the complex. The neutral structure was also confirmed by vibrational spectroscopy, as no proton transfer was observed. The diffraction studies also revealed two polymorph modifications: room temperature (α) and low temperature (ß), with a phase transition at approximately 4.9 °C. The calculated vibrational spectra are in satisfactory agreement with the experimental spectra. A comparison of the structure and the vibrational spectra between the ADAD and the oxalic acid dihydrate reveals some interesting details. The crystal structures of both crystal hydrates are almost identical; only the O…O distances of the strongest hydrogen bonds differ by 0.08 Å. Although it was expected that a larger O…O spacing in the ADAD crystal may significantly change the infrared and Raman spectra, especially for the frequency and the shape of the acidic OH stretching vibration, both the shape and frequency are almost identical, with all subpeaks topped on the broad OH stretching vibration. The O…O distance dependent are only in- and out-of-plane OH deformations modes. The presence of polarons due to the ionized defects was not observed in the vibrational spectra of ADAD. Therefore, the origin of the broad OH band shape was explained in a similar way to the acid dimers. The anharmonicity of a potential enhances the coupling of the OH stretching with the low-frequency hydrogen bond stretching, which, in addition to the Fermi resonance, structures the band shape of the OH stretching. The fine structure found as a superposition of a broad OH stretching is attributed to Davydov coupling.

1,8-dihydroxy naphthalene (DHN) - melanin confers tolerance to cadmium in isolates of melanised dark septate endophytes.

The contribution of 1,8-dihydroxy naphthalene (DHN) melanin to cadmium (Cd) tolerance in two dark septate endophytes (DSE) of the genus Cadophora with different melanin content was investigated in vitro. The DSE isolate Cad#148 with higher melanin content showed higher tolerance to Cd than the less melanised Cad#149. Melanin synthesis was significantly reduced by Cd in both isolates with uninhibited melanin synthesis, in a dose-dependent manner. Inhibition of melanin synthesis by tricyclazole reduced the relative growth of Cad#148 exposed to Cd and did not affect Cad#149. Cd accumulation was not altered by tricyclazole in the two isolates, but it increased catalase and reduced glutathione reductase activity in more melanised Cad#148, indicating higher stress levels. In contrast, in Cad#149 the enzyme activity was less affected by tricyclazole, indicating a more pronounced role of melanin-independent Cd tolerance mechanisms. Cd ligand environment in fungal mycelia was analysed by extended EXAFS (X-ray absorption fine structure). It revealed that Cd was mainly bound to O- and S-ligands, including hydroxyl, carboxyl, phosphate and thiol groups. A similar proportion of S- and O- ligands (~35% and ~65%) were found in both isolates with uninhibited melanin synthesis. Among O-ligands two types with Cd-O-C- and Cd-O-P- coordination were identified. Tricyclazole altered Cd-O- ligand environment in both fungal isolates by reducing the proportion of Cd-O-C- and increasing the proportion of Cd-O-P coordination. DHN-melanin, among other tolerance mechanisms, significantly contributes to Cd tolerance in more melanised DSE fungi by immobilising Cd to hydroxyl groups and maintaining the integrity of the fungal cell wall.

Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions.

The Nerve Growth Factor (NGF) neurotrophin acts in the maintenance and growth of neuronal populations. Despite the detailed knowledge of NGF's role in neuron physiology, the structural and mechanistic determinants of NGF bioactivity modulated by essential endogenous ligands are still lacking. We present the results of an integrated structural and advanced computational approach to characterize the extracellular ATP-NGF interaction. We mapped by NMR the interacting surface and ATP orientation on NGF and revealed the functional role of this interaction in the binding to TrkA and p75NTR receptors by SPR. The role of divalent ions was explored in conjunction with ATP. Our results pinpoint ATP as a likely transient molecular modulator of NGF signaling, in health and disease states.

The Finite Size Effects and Two-State Paradigm of Protein Folding.

The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the k2 measure, defined as the ratio of van 't Hoff and calorimetric enthalpy is related to the degeneracy of the denatured state and describes the number of cooperative units involved in the transition; additionally, it is found that the widely discussed k2=1 is just the necessary condition to classify the protein as the two-state folder. We also find that Ωc, a quantity not limited from above and growing with system size, is simply proportional to the square of the transition interval. This fact allows us to perform the classical size scaling analysis of the coil-globule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding.

Infrared spectra of hydrogen bond network in lamellar perfluorocarboxylic acid monohydrates.

The infrared spectra of the long-chain perfluorocarboxylic acid monohydrates differ markedly from those of the anhydrous dimers. Consequently, the structure of the solid perfluorocarboxylic acid monohydrates must differ from any known dimer-containing carboxylic acid crystals. Consideration of the significant features of the infrared spectra of the long-chain perfluorocarboxylic acid monohydrates, supplemented by their Raman spectra, and comparison with the spectra of auxiliary substances have led us to conclude that the rather strong neutral carboxyl-hydroxyl to water bonding can best explain the observations. The infrared spectra indicate the presence of fairly short hydrogen bonds connecting the water molecules to the carbonyl groups. In the construction of the hydrogen bonding pattern of the perfluorocarboxylic acid monohydrates, the oxalic acid dihydrate plays the key role. The striking similarity between the infrared spectra of the oxalic acid dihydrates and the perfluorocarboxylic acid monohydrates in the regions characteristic of water and OH⋯O vibration suggests that the structure of the hydrated carboxyl groups is the same in both crystals. These regions are characterized by the sharp doublet at 3539 cm-1 and 3464 cm-1, which is due to the H2O ν1 and ν3 stretching vibrations, respectively, and the broad absorption between 3000 cm-1 and 1500 cm-1 with the intense band at 1970 cm-1, both associated with the vibration of the OH⋯O group. The later peak consists of two band components at near 1980 cm-1 and 2020 cm-1. These band components show different behaviour when the temperature, polarization or deuteration is changed. In general, the infrared spectra of long-chain perfluorocarboxylic acids represent the system with very short hydrogen bonds connecting the water molecules to the carboxylates. This hydrogen bond pattern should be very similar to that found in the crystals of α-oxalic acid dihydrate.

Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins.

Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.

Redox Mechanisms in Li and Mg Batteries Containing Poly(phenanthrene quinone)/Graphene Cathodes using Operando ATR-IR Spectroscopy.

The redox reaction mechanism of a poly(phenanthrene quinone)/graphene composite (PFQ/rGO) was investigated using operando attenuated total reflection infrared (ATR-IR) spectroscopy during cycling of Li and Mg batteries. The reference phenanthrene quinone and the Li and Mg salts of the hydroquinone monomers were synthesized and their IR spectra were measured. Additionally, IR spectra were calculated using DFT. A comparison of all three spectra allowed us to accurately assign the C=O and C-O- vibration bands and confirm the redox mechanism of the quinone/Li salt of hydroquinone, with radical anion formation as the intermediate product. PFQ/rGO also showed exceptional performance in an Mg battery: A potential of 1.8 V versus Mg/Mg2+ , maximum capacity of 186 mAh g-1 (335 Wh kg-1 of cathode material), and high capacity retention with only 8 % drop/100 cycles. Operando ATR-IR spectroscopy was performed in a Mg/organic system, revealing an analogous redox mechanism to a Li/organic cell.

Analysis of the polarized IR reflectance spectra of the monoclinic α-oxalic acid dihydrate.

In contrast to the extensive molecular and crystal structure investigations on oxalic acid dihydrate (C2H2O4·2H2O, α-POX) and its deuterated analogues (α-DOX), stands the absence of a complete vibrational spectra analysis. Such analysis is desirable in view of the proton dynamics in α-POX crystals. In this communication we report the room temperature polarized IR reflectance spectra of a single crystal of α-POX recorded from the ac crystal plane, and from the plane containing the b-crystallographic axis, with polarization along the axis. Dispersion analysis of the reflectance spectra of both Bu and Au symmetry type modes, using model dielectric and reflectance function valid for the monoclinic case, have been performed and the results are discussed. Some aspects of the obtained fit results for some of the spectral regions and the peculiar change of the reflectance function with polarization angle are also discussed in this work. A correlation between the crystal structure and measured spectra, together with the results of the performed dispersion analysis, gave answers to some of the problems concerned with the orientation of the transition dipole moments of the IR active modes. The assignment of modes is assisted by DFT calculations. Another aspect covered in this work is the model reflectance functions using different averaging theories that have been applied in obtaining the reflectance spectrum of a polycrystalline sample. The results of the comparison between these spectra and the recorded reflectance spectra from a polycrystalline sample were further discussed.

Probing electrochemical reactions in organic cathode materials via in operando infrared spectroscopy.

Organic materials are receiving an increasing amount of attention as electrode materials for future post lithium-ion batteries due to their versatility and sustainability. However, their electrochemical reaction mechanism has seldom been investigated. This is a direct consequence of a lack of straightforward and broadly available analytical techniques. Herein, a straightforward in operando attenuated total reflectance infrared spectroscopy method is developed that allows visualization of changes of all infrared active bands that occur as a consequence of reduction/oxidation processes. In operando infrared spectroscopy is applied to the analysis of three different organic polymer materials in lithium batteries. Moreover, this in operando method is further extended to investigation of redox reaction mechanism of poly(anthraquinonyl sulfide) in a magnesium battery, where a reduction of carbonyl bond is demonstrated as a mechanism of electrochemical activity. Conclusions done by the in operando results are complemented by synthesis of model compound and density functional theory calculation of infrared spectra.

Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes.

Hydrophobicity plays an important role in numerous physicochemical processes from the process of dissolution in water to protein folding, but its origin at the fundamental level is still unclear. The classical view of hydrophobic hydration is that, in the presence of a hydrophobic solute, water forms transient microscopic "icebergs" arising from strengthened water hydrogen bonding, but there is no experimental evidence for enhanced hydrogen bonding and/or icebergs in such solutions. Here, we have used the redshifts and line shapes of the isotopically decoupled IR oxygen-deuterium (O-D) stretching mode of HDO water near small purely hydrophobic solutes (methane, ethane, krypton, and xenon) to study hydrophobicity at the most fundamental level. We present unequivocal and model-free experimental proof for the presence of strengthened water hydrogen bonds near four hydrophobic solutes, matching those in ice and clathrates. The water molecules involved in the enhanced hydrogen bonds display extensive structural ordering resembling that in clathrates. The number of ice-like hydrogen bonds is 10-15 per methane molecule. Ab initio molecular dynamics simulations have confirmed that water molecules in the vicinity of methane form stronger, more numerous, and more tetrahedrally oriented hydrogen bonds than those in bulk water and that their mobility is restricted. We show the absence of intercalating water molecules that cause the electrostatic screening (shielding) of hydrogen bonds in bulk water as the critical element for the enhanced hydrogen bonding around a hydrophobic solute. Our results confirm the classical view of hydrophobic hydration.

Evidence of Polaron Excitations in Low Temperature Raman Spectra of Oxalic Acid Dihydrate.

Low temperature Raman spectra of oxalic acid dihydrate (8-300 K) for both the polycrystalline and single crystal phase show strong variation with temperature in the interval from 1200 to 2000 cm(-1). Previous low temperature diffraction studies all confirmed the stability of the crystal P21/n phase with no indications of any phase transition, reporting the existence of a strong hydrogen bond between the oxalic acid and a water molecule. A new group of Raman bands in the 1200-1300 cm(-1) interval below 90 K is observed, caused by possible loss of the center of inversion. This in turn could originate either due to disorder in hydroxyl proton positions or due to proton transfer from carboxylic group to water molecule. The hypothesis of proton transfer is further supported by the emergence of new bands centered at 1600 and 1813 cm(-1), which can be explained with vibrations of H3O(+) ions. The broad band at 1600 cm(-1) looses intensity, while the band at 1813 cm(-1) gains intensity on cooling. The agreement between quantum calculations of vibrational spectra and experimentally observed Raman bands of hydronium ions in oxalic acid sesquihydrate crystal corroborates this hypothesis.

The N-Terminal Peptides of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion Channel Have Different Helical Propensities.

The voltage-dependent anion channel (VDAC) is the main mitochondrial porin allowing the exchange of ions and metabolites between the cytosol and the mitochondrion. In addition, VDAC was found to actively interact with proteins playing a fundamental role in the regulation of apoptosis and being of central interest in cancer research. VDAC is a large transmembrane ß-barrel channel, whose N-terminal helical fragment adheres to the channel interior, partially closing the pore. This fragment is considered to play a key role in protein stability and function as well as in the interaction with apoptosis-related proteins. Three VDAC isoforms are differently expressed in higher eukaryotes, for which distinct and complementary roles are proposed. In this work, the folding propensity of their N-terminal fragments has been compared. By using multiple spectroscopic techniques, and complementing the experimental results with theoretical computer-assisted approaches, we have characterized their conformational equilibrium. Significant differences were found in the intrinsic helical propensity of the three peptides, decreasing in the following order: hVDAC2 > hVDAC3 > hVDAC1. In light of the models proposed in the literature to explain voltage gating, selectivity, and permeability, as well as interactions with functionally related proteins, our results suggest that the different chemicophysical properties of the N-terminal domain are possibly correlated to different functions for the three isoforms. The overall emerging picture is that a similar transmembrane water accessible conduit has been equipped with not identical domains, whose differences can modulate the functional roles of the three VDAC isoforms.

The amide III vibrational circular dichroism band as a probe to detect conformational preferences of alanine dipeptide in water.

The conformational preferences of blocked alanine dipeptide (ADP), Ac-Ala-NHMe, in aqueous solution were studied using vibrational circular dichroism (VCD) together with density functional theory (DFT) calculations. DFT calculations of three most representative conformations of ADP surrounded by six explicit water molecules immersed in a dielectric continuum have proven high sensitivity of amide III VCD band shape that is characteristic for each conformation of the peptide backbone. The polyproline II (PII ) and αR conformation of ADP are associated with a positive VCD band while ß conformation has a negative VCD band in amide III region. Knowing this spectral characteristic of each conformation allows us to assign the experimental amide III VCD spectrum of ADP. Moreover, the amide III region of the VCD spectrum was used to determine the relative populations of conformations of ADP in water. Based on the interpretation of the amide III region of VCD spectrum we have shown that dominant conformation of ADP in water is PII which is stabilized by hydrogen bonded water molecules between CO and NH groups on the peptide backbone.