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1.
Anal Chem ; 95(46): 17037-17045, 2023 11 21.
Artigo em Inglês | MEDLINE | ID: mdl-37939225

RESUMO

Protein-drug interactions in the human bloodstream are important factors in applications ranging from drug design, where protein binding influences efficacy and dose delivery, to biomedical diagnostics, where rapid, quantitative measurements could guide optimized treatment regimes. Current measurement approaches use multistep assays, which probe the protein-bound drug fraction indirectly and do not provide fundamental structural or dynamic information about the in vivo protein-drug interaction. We demonstrate that ultrafast 2D-IR spectroscopy can overcome these issues by providing a direct, label-free optical measurement of protein-drug binding in blood serum samples. Four commonly prescribed drugs, known to bind to human serum albumin (HSA), were added to pooled human serum at physiologically relevant concentrations. In each case, spectral changes to the amide I band of the serum sample were observed, consistent with binding to HSA, but were distinct for each of the four drugs. A machine-learning-based classification of the serum samples achieved a total cross-validation prediction accuracy of 92% when differentiating serum-only samples from those with a drug present. Identification on a per-drug basis achieved correct drug identification in 75% of cases. These unique spectroscopic signatures of the drug-protein interaction thus enable the detection and differentiation of drug containing samples and give structural insight into the binding process as well as quantitative information on protein-drug binding. Using currently available instrumentation, the 2D-IR data acquisition required just 1 min and 10 µL of serum per sample, and so these results pave the way to fast, specific, and quantitative measurements of protein-drug binding in vivo with potentially invaluable applications for the development of novel therapies and personalized medicine.


Assuntos
Albumina Sérica , Soro , Humanos , Albumina Sérica/química , Soro/metabolismo , Albumina Sérica Humana/química , Ligação Proteica , Análise Espectral , Preparações Farmacêuticas , Sítios de Ligação
2.
Analyst ; 147(15): 3464-3469, 2022 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-35833538

RESUMO

Binding of drugs to blood serum proteins can influence both therapeutic efficacy and toxicity. The ability to measure the concentrations of protein-bound drug molecules quickly and with limited sample preparation could therefore have considerable benefits in biomedical and pharmaceutical applications. Vibrational spectroscopies provide data quickly but are hampered by complex, overlapping protein amide I band profiles and water absorption. Here, we show that two-dimensional infrared (2D-IR) spectroscopy can achieve rapid detection and quantification of paracetamol binding to serum albumin in blood serum at physiologically-relevant levels with no additional sample processing. By measuring changes to the amide I band of serum albumin caused by structural and dynamic impacts of paracetamol binding we show that drug concentrations as low as 7 µM can be detected and that the availability of albumin for paracetamol binding is less than 20% in serum samples, allowing identification of paracetamol levels consistent with a patient overdose.


Assuntos
Acetaminofen , Soro , Amidas , Proteínas Sanguíneas , Humanos , Albumina Sérica , Espectrofotometria Infravermelho
3.
Phys Chem Chem Phys ; 24(40): 24767-24783, 2022 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-36200672

RESUMO

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of Escherichia coli Hyd-1 (EcHyd-1) reveals the structural and dynamic influence of the protein scaffold on the Fe(CO)(CN)2 unit of the active site. Measurements on as-isolated EcHyd-1 probed a mixture of active site states including two, which we assign to Nir-SI/II, that have not been previously observed in the E. coli enzyme. Explicit assignment of carbonyl (CO) and cyanide (CN) stretching bands to each state is enabled by 2D-IR. Energies of vibrational levels up to and including two-quantum vibrationally excited states of the CO and CN modes have been determined along with the associated vibrational relaxation dynamics. The carbonyl stretching mode potential is well described by a Morse function and couples weakly to the cyanide stretching vibrations. In contrast, the two CN stretching modes exhibit extremely strong coupling, leading to the observation of formally forbidden vibrational transitions in the 2D-IR spectra. We show that the vibrational relaxation times and structural dynamics of the CO and CN ligand stretching modes of the enzyme active site differ markedly from those of a model compound K[CpFe(CO)(CN)2] in aqueous solution and conclude that the protein scaffold creates a unique biomolecular environment for the NiFe site that cannot be represented by analogy to simple models of solvation.


Assuntos
Hidrogenase , Hidrogenase/química , Domínio Catalítico , Escherichia coli/metabolismo , Ligantes , Cianetos/química , Espectrofotometria Infravermelho/métodos , Proteínas
4.
J Chem Phys ; 157(20): 205102, 2022 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-36456246

RESUMO

The ability of two-dimensional infrared (2D-IR) spectroscopy to measure the amide I band of proteins in H2O rather than D2O-based solvents by evading the interfering water signals has enabled in vivo studies of proteins under physiological conditions and in biofluids. Future exploitation of 2D-IR in analytical settings, from diagnostics to protein screening, will, however, require comparisons between multiple datasets, necessitating control of data collection protocols to minimize measurement-to-measurement inconsistencies. Inspired by analytical spectroscopy applications in other disciplines, we describe a workflow for pre-processing 2D-IR data that aims to simplify spectral cross-comparisons. Our approach exploits the thermal water signal that is collected simultaneously with, but is temporally separated from the amide I response to guide custom baseline correction and spectral normalization strategies before combining them with Principal Component noise reduction tools. Case studies show that application of elements of the pre-processing workflow to previously published data enables improvements in quantification accuracy and detection limits. We subsequently apply the complete workflow in a new pilot study, testing the ability of a prototype library of 2D-IR spectra to quantify the four major protein constituents of blood serum in a single, label-free measurement. These advances show progress toward the robust data handling strategies that will be necessary for future applications of 2D-IR to pharmaceutical or biomedical problems.


Assuntos
Amidas , Água , Projetos Piloto , Espectrofotometria Infravermelho , Solventes
5.
Health Promot Int ; 37(1)2022 Feb 17.
Artigo em Inglês | MEDLINE | ID: mdl-34244758

RESUMO

The mining industry is a demanding context for workplace health education due to a range of factors including productivity targets, workforce diversity and work roster schedules. This project investigated the impact of digital story health communication on worker engagement and its effect on interactive and critical health literacy indicators. The study comprised a quasi-experimental parallel time series research design, with control and intervention groups at each of the mine sites (n = 2). Workers in the intervention group (n = 85) received a 'toolbox talk' presentation incorporating a digital story featuring a mining industry worker and a leading cardiovascular health expert. The control group (n = 90) received equivalent health information communicated in a non-narrative manner, reflective of typical practices within the mining industry. A significantly greater effect was evident for worker engagement within the intervention group, with substantial maintenance over the follow-up period, compared with no significant effect at follow-up within the control group. Significant effects on interactive health literacy indicators (n = 3) were evident for the intervention group with corresponding lower level or nil effects within the control group. The findings highlight the benefits of evidence-based digital stories as an efficient and efficacious worker-centred health communication strategy for complex industrial workplace environments.


This quasi-experimental intervention study sought to test the effectiveness of digital stories featuring mining workers and leading health experts as a workplace health education strategy. The mining industry is a challenging setting for health education due to a range of reasons including productivity targets, workforce diversity and work roster schedules. Workers in the intervention group received a 'toolbox talk' presentation including a digital story. Workers in the control group received the same health information without the digital story, reflecting common health communication practices in the industry. Outcomes of this research demonstrate that digital storytelling was more effective on worker engagement and interactive health literacy, with a promising level of maintenance over a follow-up period. The findings show the benefits of digital storytelling as a worker focused health education strategy for complex industrial settings where time efficient communication methods are required.


Assuntos
Comunicação em Saúde , Letramento em Saúde , Austrália , Educação em Saúde , Humanos , Grupos Populacionais
6.
Int J Mol Sci ; 23(23)2022 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-36499181

RESUMO

The purpose of this study is to determine whether age-related changes to tendon matrix molecules can be detected using Raman spectroscopy. Raman spectra were collected from human Achilles (n = 8) and tibialis anterior (n = 8) tendon tissue excised from young (17 ± 3 years) and old (72 ± 7 years) age groups. Normalised Raman spectra underwent principal component analysis (PCA), to objectively identify differences between age groups and tendon types. Certain Raman band intensities were correlated with levels of advanced glycation end-product (AGE) collagen crosslinks, quantified using conventional destructive biochemistry techniques. Achilles and tibialis anterior tendons in the old age group demonstrated significantly higher overall Raman intensities and fluorescence levels compared to young tendons. PCA was able to distinguish young and old age groups and different tendon types. Raman intensities differed significantly for several bands, including those previously associated with AGE crosslinks, where a significant positive correlation with biochemical measures was demonstrated. Differences in Raman spectra between old and young tendon tissue and correlation with AGE crosslinks provides the basis for quantifying age-related chemical modifications to tendon matrix molecules in intact tissue. Our results suggest that Raman spectroscopy may provide a powerful tool to assess tendon health and vitality in the future.


Assuntos
Tendão do Calcâneo , Análise Espectral Raman , Humanos , Análise Espectral Raman/métodos , Colágeno , Produtos Finais de Glicação Avançada , Músculo Esquelético
7.
Anal Chem ; 93(2): 920-927, 2021 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-33295755

RESUMO

Glycine (Gly) is used as a model system to evaluate the ability of ultrafast two-dimensional infrared (2D-IR) spectroscopy to detect and quantify the low-molecular-weight proteinaceous components of blood serum. Combining data acquisition schemes to suppress absorption bands of H2O that overlap with the protein amide I band with analysis of peak patterns appearing in the off-diagonal region of the 2D-IR spectrum allows separation of the Gly spectral signature from that of the dominant protein fraction of serum in a transmission-mode 2D-IR measurement without any sample manipulation, e.g., filtration or drying. 2D-IR spectra of blood serum samples supplemented with varying concentrations of Gly were obtained, and a range of data analysis methods compared, leading to a detection limit of ∼3 mg/mL for Gly. The reported methodology provides a platform for a critical assessment of the sensitivity of 2D-IR for measuring the concentrations of amino acids, peptides, and low-molecular-weight proteins present in serum samples. We conclude that, in the case of several clinically relevant diagnostic molecules and their combinations, the potential exists for 2D-IR to complement IR absorption methods as the benefits of the second frequency dimension offered by 2D-IR spectroscopy outweigh the added technical complexity of the measurement.


Assuntos
Glicina/sangue , Animais , Cavalos , Espectrofotometria Infravermelho
8.
Phys Chem Chem Phys ; 23(28): 15352-15363, 2021 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-34254612

RESUMO

Changes in the structural dynamics of double stranded (ds)DNA upon ligand binding have been linked to the mechanism of allostery without conformational change, but direct experimental evidence remains elusive. To address this, a combination of steady state infrared (IR) absorption spectroscopy and ultrafast temperature jump IR absorption measurements has been used to quantify the extent of fast (∼100 ns) fluctuations in (ds)DNA·Hoechst 33258 complexes at a range of temperatures. Exploiting the direct link between vibrational band intensities and base stacking shows that the absolute magnitude of the change in absorbance caused by fast structural fluctuations following the temperature jump is only weakly dependent on the starting temperature of the sample. The observed fast dynamics are some two orders of magnitude faster than strand separation and associated with all points along the 10-base pair duplex d(GCATATATCC). Binding the Hoechst 33258 ligand causes a small but consistent reduction in the extent of these fast fluctuations of base pairs located outside of the ligand binding region. These observations point to a ligand-induced reduction in the flexibility of the dsDNA near the binding site, consistent with an estimated allosteric propagation length of 15 Å, about 5 base pairs, which agrees well with both molecular simulation and coarse-grained statistical mechanics models of allostery leading to cooperative ligand binding.


Assuntos
DNA/química , Sítio Alostérico , Pareamento de Bases , Sequência de Bases , Bisbenzimidazol/química , Cinética , Ligantes , Modelos Moleculares , Conformação de Ácido Nucleico , Espectrofotometria Infravermelho , Temperatura
9.
J Chem Phys ; 154(13): 134502, 2021 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-33832238

RESUMO

Using ultrafast two-dimensional infrared spectroscopy (2D-IR), a vibrational probe (thiocyanate, SCN-) was used to investigate the hydrogen bonding network of the protic ionic liquid ethyl-ammonium nitrate (EAN) in comparison to H2O. The 2D-IR experiments were performed in both parallel (⟨ZZZZ⟩) and perpendicular (⟨ZZXX⟩) polarizations at room temperature. In EAN, the non-Gaussian lineshape in the FTIR spectrum of SCN- suggests two sub-ensembles. Vibrational relaxation rates extracted from the 2D-IR spectra provide evidence of the dynamical differences between the two sub-ensembles. We support the interpretation of two sub-ensembles with response function simulations of two overlapping bands with different vibrational relaxation rates and, otherwise, similar dynamics. The measured rates for spectral diffusion depend on polarization, indicating reorientation-induced spectral diffusion (RISD). A model of restricted molecular rotation (wobbling in a cone) fully describes the observed spectral diffusion in EAN. In H2O, both RISD and structural spectral diffusion contribute with similar timescales. This complete characterization of the dynamics at room temperature provides the basis for the temperature-dependent measurements in Paper II of this series.

10.
Anal Chem ; 92(4): 3463-3469, 2020 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-31985198

RESUMO

Ultrafast two-dimensional infrared (2D-IR) spectra can now be obtained in a matter of seconds, opening up the possibility of high-throughput screening applications of relevance to the biomedical and pharmaceutical sectors. Determining quantitative information from 2D-IR spectra recorded on different samples and different instruments is however made difficult by variations in beam alignment, laser intensity, and sample conditions. Recently, we demonstrated that 2D-IR spectroscopy of the protein amide I band can be performed in aqueous (H2O) rather than deuterated (D2O) solvents, and we now report a method that uses the magnitude of the associated thermal response of H2O as an internal normalization standard for 2D-IR spectra. Using the water response, which is temporally separated from the protein signal, to normalize the spectra allows significant reduction of the impact of measurement-to-measurement fluctuations on the data. We demonstrate that this normalization method enables creation of calibration curves for measurement of absolute protein concentrations and facilitates reproducible difference spectroscopy methodologies. These advances make significant progress toward the robust data handling strategies that will be essential for the realization of automated spectral analysis tools for large scale 2D-IR screening studies of protein-containing solutions and biofluids.


Assuntos
Soroalbumina Bovina/análise , Temperatura , Água/química , gama-Globulinas/análise , Animais , Calibragem , Bovinos , Humanos , Solventes/química , Espectrofotometria Infravermelho
11.
Bioorg Med Chem ; 28(19): 115684, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-32912434

RESUMO

A series of combretastatin derivatives were designed and synthesised by a two-step stereoselective synthesis by use of Wittig olefination followed by Suzuki cross-coupling. Interestingly, all new compounds (2a-2i) showed potent cell-based antiproliferative activities in nanomolar concentrations. Among the compounds, 2a, 2b and 2e were the most active across three cancer cell lines. In addition, these compounds inhibited the polymerisation of tubulin in vitro more efficiently than CA-4. They caused cell cycle arrest in G2/M phase further confirming their ability to inhibit tubulin polymerisation.


Assuntos
Antineoplásicos/farmacologia , Estilbenos/farmacologia , Moduladores de Tubulina/farmacologia , Tubulina (Proteína)/metabolismo , Antineoplásicos/síntese química , Antineoplásicos/química , Pontos de Checagem do Ciclo Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Estrutura Molecular , Polimerização/efeitos dos fármacos , Estereoisomerismo , Estilbenos/síntese química , Estilbenos/química , Relação Estrutura-Atividade , Moduladores de Tubulina/síntese química , Moduladores de Tubulina/química
12.
Int J Mol Sci ; 21(6)2020 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-32245089

RESUMO

The lack of clinical detection tools at the molecular level hinders our progression in preventing age-related tendon pathologies. Raman spectroscopy can rapidly and non-invasively detect tissue molecular compositions and has great potential for in vivo applications. In biological tissues, a highly fluorescent background masks the Raman spectral features and is usually removed during data processing, but including this background could help age differentiation since fluorescence level in tendons increases with age. Therefore, we conducted a stepwise analysis of fluorescence and Raman combined spectra for better understanding of the chemical differences between young and old tendons. Spectra were collected from random locations of vacuum-dried young and old equine tendon samples (superficial digital flexor tendon (SDFT) and deep digital flexor tendon (DDFT), total n = 15) under identical instrumental settings. The fluorescence-Raman spectra showed an increase in old tendons as expected. Normalising the fluorescence-Raman spectra further indicated a potential change in intra-tendinous fluorophores as tendon ages. After fluorescence removal, the pure Raman spectra demonstrated between-group differences in CH2 bending (1450 cm-1) and various ring-structure and carbohydrate-associated bands (1000-1100 cm-1), possibly relating to a decline in cellular numbers and an accumulation of advanced glycation end products in old tendons. These results demonstrated that Raman spectroscopy can successfully detect age-related tendon molecular differences.


Assuntos
Envelhecimento/patologia , Análise Espectral Raman , Traumatismos dos Tendões/diagnóstico por imagem , Tendões/diagnóstico por imagem , Animais , Cavalos , Análise de Componente Principal , Traumatismos dos Tendões/patologia , Tendões/patologia
13.
Anal Chem ; 90(4): 2732-2740, 2018 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-29359920

RESUMO

Two-dimensional infrared spectroscopy (2D-IR) is well established as a specialized, high-end technique for measuring structural and solvation dynamics of biological molecules. Recent technological developments now make it possible to acquire time-resolved 2D-IR spectra within seconds, and this opens up the possibility of screening-type applications comparing spectra spanning multiple samples. However, such applications bring new challenges associated with finding accurate, efficient methodologies to analyze large data sets in a timely, informative manner. Here, we demonstrate such an application by screening 2016 2D-IR spectra of 12 double-stranded DNA oligonucleotides obtained in the presence and absence of binding therapeutic molecule Hoechst 33258. By applying analysis of variance combined with principal component analysis (ANOVA-PCA) to 2D-IR data for the first time, we demonstrate the ability to efficiently retrieve the base composition of a DNA sequence and discriminate ligand-DNA complexes from unbound sequences. We further show accurate differentiation of the induced-fit and rigid-body binding modes that is key to identifying optimal binding interactions of Hoechst 33258, while ANOVA-PCA results across the full sequence range correlate directly with thermodynamic indicators of ligand-binding strength that require significantly longer data acquisition times to obtain.


Assuntos
DNA/química , Análise de Componente Principal , Análise de Variância , Ligantes , Espectrofotometria Infravermelho
14.
Phys Chem Chem Phys ; 20(44): 27778-27790, 2018 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-30378611

RESUMO

The photoisomerisation of non-toxic trans-combretastatin CA4 to its cytotoxic cis isomer demonstrates the high potential of this and similar compounds for localised cancer therapy. The introduction of intramolecular charge-transfer character by altering the substituents of combretastatin systems opens up possibilities to tailor these stilbene derivatives to the special demands of anticancer drugs. In this TDDFT study we explore how absorption wavelengths for both the trans and cis isomers can be red shifted to enable deeper light penetration into tissue and how the trans → cis and cis → trans isomerisations are affected by charge transfer effects to different degrees.


Assuntos
Antineoplásicos/química , Modelos Moleculares , Neoplasias/tratamento farmacológico , Estilbenos/química , Antineoplásicos/uso terapêutico , Bibenzilas/química , Humanos , Isomerismo , Luz , Estrutura Molecular , Processos Fotoquímicos , Estilbenos/uso terapêutico , Relação Estrutura-Atividade , Termodinâmica
15.
BMC Health Serv Res ; 18(1): 956, 2018 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-30541530

RESUMO

BACKGROUND: Acute hospital services account for the largest proportion of health care system budgets, and older adults are the most frequent users. As a result, older people who have been recently discharged from hospital may be at greater risk of readmission. This study aims to evaluate the comparative effectiveness of transitional care interventions on unplanned hospital readmissions within 28 days, 12 weeks and 24 weeks following hospital discharge. METHOD: The present study was a randomised controlled trial (ACTRN12608000202369). The trial involved 222 participants who were recruited from medical wards in two metropolitan hospitals in Australia. Participants were eligible for inclusion if they were aged 65 years and over, admitted with a medical diagnosis and had at least one risk factor for readmission. Participants were randomised to one of four groups: standard care, exercise program only, Nurse Home visit and Telephone follow-up (N-HaT), or Exercise program and Nurse Home visit and Telephone follow-up (ExN-HaT). Socio-demographics, health and functional ability were assessed at baseline, 28 days, 12 weeks and 24 weeks. The primary outcome measure was unplanned hospital readmission which was defined as any hospital admission for an unforeseen or unplanned cause. RESULTS: Participants in the ExN-HaT or the N-HaT groups were 3.6 times and 2.6 times respectively significantly less likely to have an unplanned readmission 28 days following discharge (ExN-HaT group HR 0.28, 95% CI 0.09-0.87, p = 0.029; N-HaT group HR 0.38, 95% CI 0.13-1.07, p = 0.067). Participants in the ExN-HaT or the N-HaT groups were 2.13 and 2.63 times respectively less likely to have an unplanned readmission in the 12 weeks after discharge (ExN-HaT group HR 0.47, 95% CI 0.23-0.97, p = 0.014; N-HaT group HR 0.38, 95% CI 0.18-0.82, p = 0.040). At 24 weeks after discharge, there were no significant differences between groups. CONCLUSION: Multifaceted transitional care interventions across hospital and community settings are beneficial, with lower hospital readmission rates observed in those receiving more transitional intervention components, although only in first 12 weeks. TRIAL REGISTRATION: Australian and New Zealand Clinical Trial Registry ( ACTRN12608000202369 ).


Assuntos
Visita Domiciliar , Readmissão do Paciente , Cuidado Transicional , Atividades Cotidianas , Idoso , Idoso de 80 Anos ou mais , Austrália , Feminino , Hospitais , Humanos , Masculino , Nova Zelândia , Alta do Paciente , Modalidades de Fisioterapia , Fatores de Risco
16.
Anal Chem ; 89(20): 10898-10906, 2017 10 17.
Artigo em Inglês | MEDLINE | ID: mdl-28921967

RESUMO

Revealing the details of biomolecular processes in solution needs tools that can monitor structural dynamics over a range of time and length scales. We assess the ability of 2D-IR spectroscopy in combination with multivariate data analysis to quantify changes in secondary structure of the multifunctional calcium-binding messenger protein Calmodulin (CaM) as a function of temperature and Ca2+ concentration. Our approach produced quantitative agreement with circular dichroism (CD) spectroscopy in detecting the domain melting transitions of Ca2+-free (apo) CaM (reduction in α-helix structure by 13% (CD) and 15% (2D)). 2D-IR also allows accurate differentiation between melting transitions and generic heating effects observed in the more thermally stable Ca2+-bound (holo) CaM. The functionally relevant random-coil-α-helix transition associated with Ca2+ uptake that involves just 7-8 out of a total of 148 amino acid residues was clearly detected. Temperature-dependent Molecular Dynamics (MD) simulations show that apo-CaM exists in dynamic equilibrium with holo-like conformations, while Ca2+ uptake reduces conformational flexibility. The ability to combine quantitative structural insight from 2D-IR with MD simulations thus offers a powerful approach for measuring subtle protein conformational changes in solution.


Assuntos
Calmodulina/química , Espectrofotometria Infravermelho/métodos , Cálcio/química , Calmodulina/genética , Calmodulina/metabolismo , Dicroísmo Circular , Humanos , Simulação de Dinâmica Molecular , Estrutura Secundária de Proteína , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Temperatura
17.
J Comput Chem ; 38(16): 1362-1375, 2017 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-27868210

RESUMO

The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I region, using an exciton approach, in which a local mode basis of carbonyl stretches is considered. The role of solvent in shifting the Amide I band (by 30 to 50 cm-1 ) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.


Assuntos
Simulação de Dinâmica Molecular , Proteínas/química , Amidas/química , Modelos Teóricos , Conformação Proteica , Solventes/química , Espectrofotometria Infravermelho/métodos , Relação Estrutura-Atividade , Água/química
18.
Analyst ; 142(17): 3219-3226, 2017 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-28765845

RESUMO

The ability of Spatially Offset Raman Spectroscopy (SORS) to obtain chemically specific information from below the sample surface makes it a promising technique for non-invasive in vivo diagnosis of bone conditions by sampling bone through the skin. The depth below a surface interrogated by SORS depends on the system's optical properties and is difficult to estimate for complex bone material. This paper uses 830 nm laser excitation to investigate the influence of bone mineralization on photon migration properties in deer antler cortex, equine metacarpal cortex and whale tympanic bulla. Thin slices form each type of bone (thickness: 0.6-1.0 mm) were cut and put together on top of each other forming stacks with a total thickness of 4.1-4.7 mm. A 0.38 mm thin slice of polytetrafluoroethylene (PTFE) served as a test material for Raman signal recovery and was placed in between the individual bone slices within the stack. At SORS offsets of 8.0-9.5 mm Raman bands of materials not present in healthy bone (e.g. PTFE as an example) can be recovered through 4.4-4.7 mm of cortical bone tissue, depending on mineralization level and porosity. These findings significantly increase our understanding of SORS analysis through bones of different composition and provide information that is vital to determine the value of SORS as a medical diagnostic technique. The data serve to define which SORS offset is best deployed for the non-invasive detection of chemically specific markers associated with infection, degeneration and disease or cancer within bone.


Assuntos
Densidade Óssea , Osso e Ossos/diagnóstico por imagem , Fótons , Análise Espectral Raman , Animais , Cervos , Cornos , Cavalos , Lasers
19.
Phys Chem Chem Phys ; 19(16): 10333-10342, 2017 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-28397911

RESUMO

Changes in the structural and solvation dynamics of a 15mer AT DNA duplex upon melting of the double-helix are observed by a combination of ultrafast two-dimensional infrared (2D-IR) and optical Kerr-effect (OKE) spectroscopies. 2D-IR spectroscopy of the vibrational modes of the DNA bases reveal signature off-diagonal peaks arising from coupling and energy transfer across Watson-Crick paired bases that are unique to double-stranded DNA (ds-DNA). Spectral diffusion of specific base vibrational modes report on the structural dynamics of the duplex and the minor groove, which is predicted to contain a spine of hydration. Changes in these dynamics upon melting are assigned to increases in the degree of mobile solvent access to the bases in single-stranded DNA (ss-DNA) relative to the duplex. OKE spectra exhibit peaks that are assigned to specific long-range phonon modes of ds- and ss-DNA. Temperature-related changes in these features correlate well with those obtained from the 2D-IR spectra although the melting temperature of the ds-DNA phonon band is slightly higher than that for the Watson-Crick modes, suggesting that a degree of long-range duplex structure survives the loss of Watson-Crick hydrogen bonding. These results demonstrate that the melting of ds-DNA disrupts helix-specific structural dynamics encompassing length scales ranging from mode delocalisation in the Watson-Crick base pairs to long-range phonon modes that extend over multiple base pairs and which may play a role in molecular recognition of DNA.


Assuntos
DNA/química , Pareamento de Bases , DNA/metabolismo , Conformação de Ácido Nucleico , Transição de Fase , Solventes/química , Espectrofotometria Infravermelho , Temperatura de Transição
20.
Anal Chem ; 88(3): 1559-63, 2016 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-26761345

RESUMO

The tendons in the turkey leg have specific well-defined areas which become mineralized as the animal ages and they are a thoroughly characterized model system for studying the mineralization process of bone. In this study, nondestructive Raman spectroscopic analysis was used to explore the hypothesis that regions of the turkey tendon that are associated with mineralization exhibit distinct and observable chemical modifications of the collagen prior to the onset of mineralization. The Raman spectroscopy features associated with mineralization were identified by probing (on the micrometer scale) the transition zone between mineralized and nonmineralized regions of turkey leg tendons. These features were then measured in whole tendons and identified in regions of tendon which are destined to become rapidly mineralized around 14 weeks of age. The data show there is a site-specific difference in collagen prior to the deposition of mineral, specifically the amide III band at 1270 cm(-1) increases as the collagen becomes more ordered (increased amide III:amide I ratio) in regions that become mineralized compared to collagen destined to remain nonmineralized. If this mechanism were present in materials of different mineral fraction (and thus material properties), it could provide a target for controlling mineralization in metabolic bone disease.


Assuntos
Colágeno/química , Minerais/química , Proteínas/química , Tendões/química , Perus/anatomia & histologia , Amidas/análise , Amidas/química , Animais , Análise Espectral Raman
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