Diffusion-Enhanced Förster Resonance Energy Transfer in Flexible Peptides: From the Haas-Steinberg Partial Differential Equation to a Closed Analytical Expression.

In the huge field of polymer structure and dynamics, including intrinsically disordered peptides, protein folding, and enzyme activity, many questions remain that cannot be answered by methodology based on artificial intelligence, X-ray, or NMR spectroscopy but maybe by fluorescence spectroscopy. The theory of Förster resonance energy transfer (FRET) describes how an optically excited fluorophore transfers its excitation energy through space to an acceptor moiety-with a rate that depends on the distance between donor and acceptor. When the donor and acceptor moiety are conjugated to different sites of a flexible peptide chain or any other linear polymer, the pair could in principle report on chain structure and dynamics, on the site-to-site distance distribution, and on the diffusion coefficient of mutual site-to-site motion of the peptide chain.

Cocoa bean fingerprinting via correlation networks.

Cocoa products have a remarkable chemical and sensory complexity. However, in contrast to other fermentation processes in the food industry, cocoa bean fermentation is left essentially uncontrolled and is devoid of standardization. Questions of food authenticity and food quality are hence particularly challenging for cocoa.

Cocoa origin classifiability through LC-MS data: A statistical approach for large and long-term datasets.

Classification of food samples based upon their countries of origin is an important task in food industry for quality assurance and development of fine flavor products. Liquid chromatography -mass spectrometry (LC-MS) provides a fast technique for obtaining in-depth information about chemical composition of foods. However, in a large dataset that is gathered over a period of few years, multiple, incoherent and hard to avoid sources of variations e.

Investigating time dependent cocoa bean fermentation by ESI-FT-ICR mass spectrometry.

A cocoa bean fermentation series, comprising bean samples taken every 24 h of a seven-day cocoa fermentation was analyzed by ultra-high-resolution mass spectrometry using the ESI-FT-ICR technique. Data were acquired in both positive and negative ion mode. At early fermentation times around 2000 signals could be resolved raising to a maximum of 8000 signals in each ion mode towards the end of the fermentation.

Novel Amadori and Heyns compounds derived from short peptides found in dried cocoa beans.

Chemical transformations of Amadori compounds are responsible for the formation of aroma volatiles at the end of the Maillard reaction cascade, which in turn contributes to unique organoleptic characteristics of chocolate. A large amount of short peptides reported in fermented cocoa suggests the existence of a much larger variety of these flavor precursors than previously suspected. An HPLC-MS-MS study was performed on dried Malaysian cocoa beans to identify novel Amadori and Heyns compounds.

Experimentally modelling cocoa bean fermentation reveals key factors and their influences.

Cocoa bean fermentation still remains a rather empirical process. The research presented here employed an artificial system of fermentation, using controlled incubations, in order to achieve greater control over the external influences that cocoa beans are exposed to, with the aim of experimentally modelling changes to bean components (responses). Experimental design was used, in a first-ever attempt, to study the effects of five factors and their interactions on the profiles of pH, peptides, and flavanols in the bean during the incubations.

Thermally-induced formation of taste-active 2,5-diketopiperazines from short-chain peptide precursors in cocoa.

2,5-diketopiperazines (DKPs) are cyclic dipeptides responsible for the specific bitter taste of cocoa formed during roasting. The 2,5-diketopiperazine and peptide composition of four different cocoa bean samples from different origins were studied using LC-MS techniques. 34 diketopiperazines were identified, of which 10 are newly reported in cocoa.

Two Orders of Magnitude Variation of Diffusion-Enhanced Förster Resonance Energy Transfer in Polypeptide Chains.

A flexible peptide chain displays structural and dynamic properties that correspond to its folding and biological activity. These properties are mirrored in intrachain site-to-site distances and diffusion coefficients of mutual site-to-site motion. Both distance distribution and diffusion determine the extent of Förster resonance energy transfer (FRET) between two sites labeled with a FRET donor and acceptor.

Forcing fermentation: Profiling proteins, peptides and polyphenols in lab-scale cocoa bean fermentation.

This study encompassed the lab-scale fermentation of cocoa beans in 300-g heaps under controlled laboratory conditions, in order to replicate the microbial dynamics and metabolomic changes that usually occur in large-scale spontaneous fermentations. Growth profiles of yeast and acetic acid bacteria (AAB) with the native assortment of microbes as well as with the use of a starter culture were very similar to those observed in literature. Greater production of acetic acid by AAB not only led to more acidic-tasting liquor but also contributed to bitterness, due to polyphenol preservation.

Origin and varietal based proteomic and peptidomic fingerprinting of Theobroma cacao in non-fermented and fermented cocoa beans.

It is well known that the development of chocolate flavor is initiated during cocoa bean fermentation. Storage proteins undergo the most intensive breakdown yielding peptides and free amino acids, which both serve as flavor precursors. A comprehensive analysis of cocoa proteins and oligopeptides of non-fermented and fermented beans from various geographic origins allows the assessment of systematic differences with respect to their origin as well as fermentation status.

Degradation of cocoa proteins into oligopeptides during spontaneous fermentation of cocoa beans.

Degradation products of proteins produced during fermentation are believed to be the key precursors of a range of Maillard reactions that deliver the characteristic flavor and aroma of cocoa and chocolate. We have utilized UPLC-ESI-Q-q-TOF to identify and relatively quantify the largest collection of cocoa oligopeptides during a spontaneous fermentation time series using Ivory Coast cocoa beans. Peptides were identified, sequenced by tandem mass spectrometry and annotated based on their characteristic fragmentation pattern in the positive-ion mode.

Profiling, quantification and classification of cocoa beans based on chemometric analysis of carbohydrates using hydrophilic interaction liquid chromatography coupled to mass spectrometry.

Fifty-six cocoa bean samples from different origins and status of fermentation were analyzed by a validated hydrophilic interaction liquid chromatography-electrospray ionization-time of flight-mass spectrometry (HILIC-ESI-TOF-MS) method. The profile of the low molecular weight carbohydrate (LMWC) was analyzed by high resolution and tandem mass spectrometry, which allowed the identification of mono-, di-, tri- and tetrasaccharides, sugar alcohols and iminosugars. This study provides, for the first time in a large set of samples, a comprehensive absolute quantitative data set for the carbohydrates identified in cocoa beans (fructose, glucose, mannitol, myo-inositol, sucrose, melibiose, raffinose and stachyose).

Method-Unifying View of Loop-Formation Kinetics in Peptide and Protein Folding.

Protein folding can be described as a probabilistic succession of events in which the peptide chain forms loops closed by specific amino acid residue contacts, herein referred to as loop nodes. To measure loop rates, several photophysical methods have been introduced where a pair of optically active probes is incorporated at selected chain positions and the excited probe undergoes contact quenching (CQ) upon collision with the second probe. The quenching mechanisms involved triplet-triplet energy transfer, photoinduced electron transfer, and collision-induced fluorescence quenching, where the fluorescence of Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.

Biochemical fate of vicilin storage protein during fermentation and drying of cocoa beans.

Key cocoa-specific aroma precursors are generated during the fermentation of cocoa beans via the proteolysis of the vicilin-like globulin. Previous studies had shown that degradation of this particular 566 amino acid-long storage protein leads to three distinct subunits with different molecular masses. Although oligopeptides generated from the proteolysis of vicilin-like globulin have been studied previously, changes occurring to vicilin at different stages of fermentation have not yet been explored in detail.

Origin-based polyphenolic fingerprinting of Theobroma cacao in unfermented and fermented beans.

A comprehensive analysis of cocoa polyphenols from unfermented and fermented cocoa beans from a wide range of geographic origins was carried out to catalogue systematic differences based on their origin as well as fermentation status. This study identifies previously unknown compounds with the goal to ascertain, which of these are responsible for the largest differences between bean types. UHPLC coupled with ultra-high resolution time-of-flight mass spectrometry was employed to identify and relatively quantify various oligomeric proanthocyanidins and their glycosides amongst several other unreported compounds.

Aseptic artificial fermentation of cocoa beans can be fashioned to replicate the peptide profile of commercial cocoa bean fermentations.

The fermentation of cocoa beans is essential for the generation of flavour precursors that are required later on to form the flavour components of chocolate. From the many different precursors that are generated, oligopeptides and free amino acids comprise a significant proportion as some of them form Maillard reaction products during the roasting process. Therefore, the diversity of peptides is an important contributing factor to the quality of a fermentation which is in turn controlled by proteolytic activity within the cocoa bean, and is driven by changes in the presence of fermentation by-products as a result of microbial activity outside the bean.

The role of ligands on protein retention in adsorption chromatography: a surface energetics approach.

Protein adsorption onto hydrophobic chromatographic supports has been investigated using a colloid theory surface energetics approach. The surface properties of commercially available chromatographic beads, Toyopearl Phenyl 650-C, and Toyopearl Butyl 650-C, have been experimentally determined by contact angle and zeta potential measurements. The adsorption characteristics of these beads, which bear the same backbone matrix but harbor different ligands, have been studied toward selected model proteins, in the hydrated as well as dehydrated state.

Phase I study of the Aurora B kinase inhibitor barasertib (AZD1152) to assess the pharmacokinetics, metabolism and excretion in patients with acute myeloid leukemia.

Purpose: Barasertib (AZD1152) is a pro-drug that rapidly undergoes phosphatase-mediated cleavage in serum to release barasertib-hQPA, a selective Aurora B kinase inhibitor that has shown preliminary activity in clinical studies of patients with acute myeloid leukemia (AML). The pharmacokinetic (PK), metabolic and excretion profiles of barasertib and barasertib-hQPA were characterized in this open-label Phase I study.

Methods: Five patients with poor prognosis AML (newly diagnosed, relapsed or refractory) received barasertib 1,200 mg as a 7-day continuous infusion every 28 days.

Detection of urinary tract stones at low-radiation-dose CT with z-axis automatic tube current modulation: phantom and clinical studies.

Purpose: To evaluate depiction of urinary tract calculi at computed tomography (CT) with a z-axis modulation technique at various noise indexes to reduce radiation dose and preserve image quality.

Materials And Methods: Sixteen radiopaque kidney stones (2.5-19.

Multidetector computed tomography technology: current status and emerging developments.

By virtue of its speed and isotropic resolution of thin slices, multidetector-row computed tomography (MDCT) offers unique advantages over previous single-detector-row CT, with improved temporal and spatial resolution. This review describes the historical perspective and growth trends of MDCT scanners and highlights the current status and emerging developments in multidetector technology based on presentations at the symposium "Advances in Multidetector CT," under the auspices of the Institute for Advanced Medical Education in Washington, DC.

Evaluation of living liver transplant donors: method for precise anatomic definition by using a dedicated contrast-enhanced MR imaging protocol.

Liver transplantation from a living donor involves removal of part of the donor liver in a fashion that does not endanger its vascular supply or metabolic function. The radiologist plays an important role in evaluation of the living donor to define the conditions under which graft donation is contraindicated and to identify anatomic variations that may alter the surgical approach. In the past, diagnostic work-up of the donor involved costly and invasive tests.

Evaluation of simethicone-coated cellulose as a negative oral contrast agent for abdominal CT.

Rationale And Objectives: Because of the increased clinical use of computed tomography (CT) for imaging the abdominal vasculature and urinary tract, there is a need for negative contrast agents. The authors undertook this study to assess the suitability of simethicone-coated cellulose (SCC), which is approved for use as an oral contrast agent in sonography, for use as a negative oral contrast agent in abdominal CT.

Materials And Methods: This prospective study involved 40 adult patients scheduled to undergo abdominal CT for the evaluation of hematuria.

Comparison between low (3:1) and high (6:1) pitch for routine abdominal/pelvic imaging with multislice computed tomography.

Purpose: The purpose of this study was to compare the performance of low helical pitch acquisition (3:1) and high helical pitch acquisition (6:1) for routine abdominal/pelvic imaging with multislice computed tomography (CT).

Method: Three hundred eighty-four patients referred for abdominal/pelvic CT were examined in a breath-hold on a multislice CT scanner (LightSpeed QX/I; General Electric Medical Systems, Milwaukee, WI). Patients were randomized and scanned with pitch of 3:1 or 6:1 using a constant 140 peak kV and 280-300 mA.