On the conformation of the biotin molecule

Strzelczyk, Aleksandra; Dobrowolski, Jan Cz.; Mazurek, Aleksander P.

doi:10.1016/s0166-1280(00)00804-6

Cited by 14 publications

(23 citation statements)

References 10 publications

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“…As most of these fragments are localized on the fused ureido/tetrahydrothiophene (U/T) rings at the "head" of the biotin molecule, the presence of multiple local conformational minima along the covalent potential energy surface are made accessible by flexibility in the -C 4 H 8 -"tail" linking the fused ring head to the carboxylic acid (COOH) pendant group. While multiple local minima have been predicted by previous studies, [23][24][25] the two most interesting conformations of note are a cyclic form predicted in the gas phase (where a pair of H bonds are formed between the U/T rings and the COOH) and the fully-extended form found in the solid-state (where the formation of multiple intermolecular H bonds is preferred over intramolecular H-bond formation). 25 Figure 2 shows a sample of the identified local minima predicted to lie within 40 kJ/mol of the global minimum, as well as the least stable structure optimized to a minimum energy geometry.…”

Section: Biotinmentioning

confidence: 79%

Analysis of Diamondoid Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing Approach

Allis¹,

Helfrich²,

Freitas³

et al. 2011

Jnl of Comp & Theo Nano

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The results of a combined molecular dynamics/quantum chemistry pathology study of previously reported organic (diamondoid) tooltips for diamondoid mechanosynthesis (DMS) are presented. This study, employing the NanoHive@Home (NH@H) distributed computing project, produced 80,000 tooltip geometries used in 200,000 calculations optimized at either the RHF/3-21G or RHF/STO-3G levels of theory based on geometries obtained from high-energy molecular dynamics simulations to produce highly deformed starting geometries. These 200,000 calculations have been catalogued, grouped according to energies and geometries, and analyzed to consider potentially accessible defect structures (pathologies) for tooltip geometries either binding a carbon dimer (C 2 feedstock or not containing the transported dimer feedstock. The transport and deposition of feedstock and the stability of the tooltip between dimer "loading" cycles are important geometries that must be considered as part of a tooltip stability analysis. The NH@H framework is found to be a useful method both for the study of highly deforming covalent geometries and, using lower-temperature MD simulations, for generating and optimizing molecular conformations (demonstrated using biotin, n-heptane, and n-octane in this study). The results of the pathology survey are discussed and general considerations for the exploration of DMS tooltip usability are explored.

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Section: Biotinmentioning

confidence: 79%

Analysis of Diamondoid Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing Approach

Allis¹,

Helfrich²,

Freitas³

et al. 2011

Jnl of Comp & Theo Nano

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“…This was indicated by a time dependent red shift and subsequent broadening of the GNP SPR peak from 525 nm to about 683 nm. Agglomeration of biotinylated GNPs has been shown to be caused by hydrogen bonding between the inter-particle biotin molecules [35]. …”

Section: Resultsmentioning

confidence: 99%

Catalase-coupled gold nanoparticles: Comparison between the carbodiimide and biotin–streptavidin methods

et al. 2011

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The use of proteins for therapeutic applications requires the protein to maintain sufficient activity for the period of in vivo treatment. Many proteins exhibit a short half-life in vivo and, thus, require delivery systems for them to be applied as therapeutics. The relative biocompatibility and the ability to form functionalized bioconjugates via simple chemistry make gold nanoparticles excellent candidates as protein delivery systems. Herein, two protocols for coupling proteins to gold nanoparticles were compared. In the first, the strong biomolecular binding between biotin and streptavidin was used to couple catalase to the surface of gold nanoparticles. In the second protocol, the formation of an amide bond between carboxylic acid coated gold nanoparticles and free surface amines of catalase using carbodiimide chemistry was performed. The stability and kinetics of the different steps involved in these protocols were studied using UV-Visible spectroscopy, dynamic light scattering, and transmission electron microscopy. The addition of mercaptoundecanoic acid in conjugation with (N-(6-(biotinamido)hexyl)-3′-(2′-pyridyldithio)-propionamide increased the stability of biotinylated gold nanoparticles. Although the carbodiimide chemistry based bioconjugation approach exhibited a decrease in catalase activity, the carbodiimide chemistry based bioconjugation approach resulted in more active catalase per gold nanoparticle compared to that of mercaptoundecanoic acid stabilized biotinylated gold nanoparticles. Both coupling protocols resulted in gold nanoparticles loaded with active catalase. Thus, these gold nanoparticle systems and coupling protocols represent promising methods for the application of gold nanoparticles for protein delivery.

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“…The remaining conformers are derived from the ab initio work of Strzelczyk and coworkers. 15 A\\-transbiotin (AT) has the valeryl chain fully extended and is calculated to be lower in energy than CT. Finally, the last three biotin conformers involve intramolecular hydrogen bonds between the valeryl chain and the ureido ring of the bicyclic moiety.…”

Section: Hn Nhmentioning

confidence: 99%

“…Our calculated values for the relative gas-phase energies are consistent with those reported previously. 15 The calculated THz spectrum for each conformer is presented in Fig. 7.…”

Section: Hn Nhmentioning

confidence: 99%

Continuous-Wave Terahertz Spectroscopy of Plasmas and Biomolecules

Plusquellic

Korter

Fraser

et al. 2003

Int. J. Hi. Spe. Ele. Syst.

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Continuous-wave linear-absorption spectroscopy based on THz radiation generated by solid-state photomixers has been applied to the investigation of the dynamics of biomolecules in polyethylene matrices and to line shape studies of HF for diagnostics of semiconductor etching plasmas. The THz spectra of biotin and myoglobin have been obtained using a variable-temperature, cryogenic sampling system. The spectrum of biotin displays a small number of discrete absorptions over the temperature range from 4.2 K to room temperature while the spectrum of myoglobin has no obvious resonance structure at the >10% fractional absorption level. Spectral predictions from the lowest energy ab initio conformations of biotin are in poor agreement with experiment, suggesting the need to include condensed-phase environmental interactions for qualitative predictions of the THz spectrum. Vibrational anharmonicity is used to model the line shapes that result from drastic changes in vibrational sequence level populations of biotin over this temperature range. Anharmonicity factors (x e (o e /m e ) at the levels of 0.1 % to 0.8 % are obtained from non-linear least squares fits of the observed resonances and illustrate their important for refining model predictions. Application of the photomixer system to line shape studies in etching plasmas has been used to study the formation efficiency and translational temperature of HF at 1.2 THz under different operating conditions. These results will aid in understanding the chemistry of industry-standard fluorocarbon and oxygenated fluorocarbon etching plasmas.

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On the conformation of the biotin molecule

Cited by 14 publications

References 10 publications

Analysis of Diamondoid Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing Approach

Analysis of Diamondoid Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing Approach

Catalase-coupled gold nanoparticles: Comparison between the carbodiimide and biotin–streptavidin methods

Continuous-Wave Terahertz Spectroscopy of Plasmas and Biomolecules

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