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1

Methods of peptide conformation studies

100%

Bierzynski A.

Acta Biochimica Polonica

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2001

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tom 48

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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

CD investigations on conformation of H-X-[Pro]n-Y-OH peptides [X-Trp, Tyr; Y-Tyr, Met]; models for intramolecular long range electron transfer

88%

Wierzchowski K. L., Majcher K., Poznanski J.

Acta Biochimica Polonica

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1995

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tom 42

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nr 2

Conformations of three series of peptides: H-Trp-(Pro)n-Tyr-OH (n = 1-5), H-Trp-(Pro)n-Met-OH (n = 1-3) and H-Tyr-(Pro)n-Met-OH (n = 1-3), used as models in studies on long range electron transfer through protein matrix, were investigated by CD spectroscopy in aqueous solution at pH 5.2 in the temperature range of 10°C-90°C. CD spectra of their component N- and C-terminal dipeptide and oligoproline fragments were also measured under similar conditions. In interpretation of the spectra the cis <-> trans equilibrium about X-Pro bonds was taken into account and CD spectra of Trp-Pro and Tyr-Pro chromophores in trans and cis configuration of the peptide bond were evaluated. The spectra of n = 3-5 peptides from the first series and those with n = 2-3 from the other two series exhibit a strong negative band in the 202-207 nm region, the strength of which is proportional to the number of Pro residues in the (Pro)n bridge, and characterized by a large temperature decrement. In view of close similarity between characteristics of this band and the 206 nm band of aqueous oligoproline peptides = 3), known to attain a left handed helical conformation similar to that of 31 helix of the all-trans poly-L-proline II, this band was attributed to a conformation of the latter type. H-Trp-(Pro)2-Tyr-OH does not form this conformation due to sterical interaction between the two bulky aromatic side chains. Conclusions drawn from analysis of the CD spectra are supported by 1H and C13 NMR data reported elsewhere (Poznański et al., 1993, Biopolymers 33,781-795).

3

Circular dichroism and aggregation studies of amyloid beta [11-28] fragment and its variants

75%

Juszczyk P., Kolodziejczyk A. S., Grzonka Z.

Acta Biochimica Polonica

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2005

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tom 52

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nr 2

Aggregation of Aβ peptides is a seminal event in Alzheimer’s disease. Detailed understanding of Aβ assembly would facilitate the targeting and design of fibrillogenesis inhibitors. Here comparative conformational and aggregation studies using CD spectroscopy and thioflavine T fluorescence assay are presented. As a model peptide, the 11–28 fragment of Aβ was used. This model peptide is known to contain the core region responsible for Aβ aggregation. The structural and aggregational behaviour of the peptide was compared with the properties of its variants corresponding to natural, clinically relevant mutants at positions 21-23 (A21G, E22K, E22G, E22Q and D23N). In HFIP (hexafluoro-2-propanol), a strong α-helix inducer, the CD spectra revealed an unexpectedly high amount of β-sheet conformation. The aggregation process of Aβ(11–28) variants provoked by water addition to HFIP was found to be consistent with a model of an α-helix-containing intermediate. The aggregation propensity of all Aβ(11–28) variants was also compared and discussed.

4

Size, shape and secondary structure of calponin

75%

Czurylo E. A., Eimer W., Kulikova N., Hellweg T.

Acta Biochimica Polonica

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2000

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tom 47

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nr 3

The overall size and shape of the chicken gizzard calponin (CaP) h1 molecule was investigated by dynamic light scattering (DLS) measurements. From the DLS experiments, a z-averaged translational diffusion coefficient is derived (5.75 0.3) 10-7cm2s-1, which corresponds to a hydrodynamic radius of 3.72 nm for calponin. The frictional ratio (1.8 for the unhydrated molecule and 1.5 for the hydrated one) suggests a pronounced anisotropic structure for the molecule. An ellipsoidal model in length 19.4 nm and with a diameter of 2.6 nm used for hydrodynamic calculations was found to reproduce the DLS experimental data. The evaluation of the secondary structure of CaP h1 from the CD spectra by two independent methods has revealed that it contains, on average, 23% helix, 19% beta-strand, 18% beta-turns and loops, and 40% of remainder structures. These values are in good agreement with those predicted from the amino-acid sequence. Predictions used for CaP h1 were applied to other isoforms of known sequences and revealed that all calponins share a common secondary structure. Moreover, the predicted structure of the calponin CH domain is identical to that found by X-ray studies of the spectrin, fimbrin and utrophin CH domains.

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

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2008

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tom 55

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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

Circular dichroism analysis for multidomain proteins: studies of the irreversible unfolding of Hepatitis C virus helicase

63%

Gozdek A., Stankiewicz-Drogon A., Poznanski J., Boguszewska-Chachulska A. M.

Acta Biochimica Polonica

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2008

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tom 55

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nr 1

The non-structural protein 3 (NS3) of Hepatitis C virus (HCV) is a bifunctional enzyme with RNA-dependent NTPase/RNA helicase and serine protease activities, and thus represents a promising target for anti-HCV therapy. These functions are performed by two distinct moieties; the N-terminal protease domain and the C-terminal helicase domain that further folds into three structural subdomains. To obtain lower molecular mass proteins suitable for nuclear magnetic resonance studies of helicase-inhibitor complexes, helicase domains 1, 2, and 1+2 devoid of a hydrophobic β-loop were overexpressed and purified. Circular dichroism studies were carried out to confirm the secondary structure content and to determine thermodynamic parameters describing the stability of the proteins. Both thermal and GuHCl-induced unfolding experiments confirmed the multidomain organization of the helicase. The unfolding transition observed for domain 1+2 was in agreement with the model of two well-resolved successive steps corresponding to the independent unfolding of domains 1 and 2, respectively. In the case of the full-length helicase, the presence of domain 3 remarkably changed the transition profile, leading to fast and irreversible transformation of partially unfolded protein.

7

Structural and functional changes of bovine carbonic anhydrase as a consequence of temperature

63%

Sarraf N. S., Saboury A. A., Ranjbar B., Moosavi-Movahedi A. A.

Acta Biochimica Polonica

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2004

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tom 51

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nr 3

The temperature dependence of the activity and structure of the enzyme carbonic anhydrase was studied. The Arrhenius plot shows a jump which is seen usually in proteins with more than one subunit or with one subunit but more than one domain. Since carbonic anhydrase has only one subunit with one domain, the fine conformational changes of the protein motifs could only be detected through circular dichroism polarimetry. It seems that the jump in Arrhenius plot is a result of some slight structural changes in the secondary and tertiary structures of the enzyme.

8

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

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2001

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tom 48

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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.

Ograniczanie wyników

Methods of peptide conformation studies

CD investigations on conformation of H-X-[Pro]n-Y-OH peptides [X-Trp, Tyr; Y-Tyr, Met]; models for intramolecular long range electron transfer

Circular dichroism and aggregation studies of amyloid beta [11-28] fragment and its variants

Size, shape and secondary structure of calponin

Interaction of anesthetic supplement thiopental with human serum albumin

Circular dichroism analysis for multidomain proteins: studies of the irreversible unfolding of Hepatitis C virus helicase

Structural and functional changes of bovine carbonic anhydrase as a consequence of temperature

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