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1

Methods of peptide conformation studies

100%
Bierzynski A.
Acta Biochimica Polonica
|
2001
|
tom 48
|
nr 4
In solution most of the peptides assume multiple flexible conformations. Determina­tion of the dominant conformers and evaluation of their populations is the aim of pep- tide conformation studies, in which theoretical and experimental methods play com­plementary roles. Molecular dynamics or Monte Carlo methods are quite effective in searching the conformational space accessible to a peptide but they are not able to es­timate, precisely enough, the populations of various conformations. Therefore, they must be supplemented by experimental data. In this paper, a short review of the experimental methods, most widely used in pep­tide conformational studies, is presented. Among them NMR plays the leading role. Valuable information is also obtained from hydrogen exchange, fluorescence reso­nance energy transfer, and circular dichroism measurements. The advantages and shortcomings of these methods are discussed.
2

Fluorescence resonance energy transfer in studies of inter-chromophoric distances in biomolecules

88%
Lankiewicz L., Malicka J., Wiczk W.
Acta Biochimica Polonica
|
1997
|
tom 44
|
nr 3
Fluorescence resonance energy transfer (FRET) is a technique widely used in studies of interchromophoric distances in biomolecules such as peptides, pro­teins and nucleic acids. FRET is especially useful in determination of confor­mational changes caused by a solvent, presence of denaturing agents, diffusion and other external factors. Precision of interchromophoric distances obtained using the FRET technique is comparable with that of low-resolution X-ray diffraction and NMR data. Comparison of FRET results with the crystal struc­ture for several proteins is reviewed. Moreover, the effect of the orientation factor K2 value on FRET results and determinants of k2 are discussed.
3

Chemical synthesis of dolichyl phosphates, their analogues and derivatives and application of these compounds in biochemical assays

75%
Danilov L. L., Druzhinina T. N.
Acta Biochimica Polonica
|
2007
|
tom 54
|
nr 4
695-701
Several methods for simple and efficient chemical synthesis of dolichyl phosphates and their an-alogues and derivatives are briefly summarized with a special emphasis on chemical modifica-tion of phosphoryl group and preparation of dolichyl phosphates labelled at the ω-end and at the γ-isoprene unit of the isoprene chain by fluorescent groups, 2-aminopyridine and 1-aminon-aphtalene residues. Additionally, data on biochemical assays with application of the compounds mentioned above are presented.
4

Molecular beacons: a novel optical diagnostic tool

63%
Han S.-X., Jia X., Ma J.-L., Zhu Q.
Archivum Immunologiae et Therapiae Experimentalis
|
2013
|
tom 61
|
nr 2
5

Interaction of anesthetic supplement thiopental with human serum albumin

63%
Khan S. N., Islam B., Rajeswari M. R., Usmani H., Khan A. U.
Acta Biochimica Polonica
|
2008
|
tom 55
|
nr 2
399-409
Thiopental (TPL) is a commonly used barbiturate anesthetic. Its binding with human serum albumin (HSA) was studied to explore the anesthetic-induced protein dysfunction. The basic binding interaction was studied by UV-absorption and fluorescence spectroscopy. An increase in the binding affinity (K) and in the number of binding sites (n) with the increasing albumin concentration was observed. The interaction was conformation-dependent and the highest for the F isomer of HSA, which implicates its slow elimination. The mode of binding was characterized using various thermodynamic parameters. Domain II of HSA was found to possess a high affinity binding site for TPL. The effect of micro-metal ions on the binding affinity was also investigated. The molecular distance, r, between donor (HSA) and acceptor (TPL) was estimated by fluorescence resonance energy transfer (FRET). Correlation between the stability of the TPL-N and TPL-F complexes and drug distribution is discussed. The structural changes in the protein investigated by circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy reflect perturbation of the albumin molecule and provide an explanation for the heterogeneity of action of this anesthetic.
6

GTP-binding properties of the membrane-bound form of porcine liver annexin VI

63%
Kirilenko A., Golczak M., Pikula S., Bandorowicz-Pikula J.
Acta Biochimica Polonica
|
2001
|
tom 48
|
nr 4
Annexin VI (AnxVI) of molecular mass 68-70 kDa belongs to a multigenic family of ubiquitous Ca2+ - and phospholipid-binding proteins. In this report, we describe the GTP-binding properties of porcine liver AnxVI, determined with a fluorescent GTP analogue, 2-(or 3')-0-(2,4,6-trinitrophenyl)guanosine 5' -triphosphate (TNP-GTP). The optimal binding of TNP-GTP to AnxVI was observed in the presence of Ca2+ and asolectin liposomes, as evidenced by a 5.5-fold increase of TNP-GTP fluorescence and a concomitant blue shift (by 17 nm) of its maximal emission wavelength. Titration of AnxVI with TNP-GTP resulted in the determination of the dissociation constant (Kd) and binding stoichiometry that amounted to 1.3 uM and 1:1 TNP-GTP/AnxVI, mole/mole, respectively. In addition, the intrinsic fluorescence of the membrane- bound form of AnxVI was quenched by TNP-GTP and this was accompanied by fluo­rescence resonance energy transfer (FRET) from AnxVI Trp residues to TNP-GTP. This indicates that the GTP-binding site within the AnxVI molecule is probably located in the vicinity of a Trp-containing domain of the protein. By controlled proteolysis of human recombinant AnxVI, followed by purification of the proteolytic fragments by affinity chromatography on GTP-agarose, we isolated a 35 kDa fragment correspond­ing to the N-terminal half of AnxVI containing Trp192 . On the basis of these results, we suggest that AnxVI is a GTP-binding protein and the binding of the nucleotide may have a regulatory impact on the interaction of annexin with membranes, e.g. forma­tion of ion channels by the protein.
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