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Varga F, Drzík M, Handl M, Chlpík J, Kos P, Filová E, Rampichová M, Necas A, Trc T, Amler E. Biomechanical characterization of cartilages by a novel approach of blunt impact testing. Physiol Res 2007; 56 Suppl 1:S61-S68. [PMID: 17552893 DOI: 10.33549/physiolres.931303] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The present article introduces a novel method of characterizing the macromechanical cartilage properties based on dynamic testing. The proposed approach of instrumented impact testing shows the possibility of more detailed investigation of the acting dynamic forces and corresponding deformations within the wide range of strain rates and loads, including the unloading part of stress-strain curves and hysteresis loops. The presented results of the unconfined compression testing of both the native joint cartilage tissues and potential substitute materials outlined the opportunity to measure the dissipation energy and thus to identify the initial mechanical deterioration symptoms and to introduce a better definition of material damage. Based on the analysis of measured specimen deformation, the intact and pathologically changed cartilage tissue can be distinguished and the differences revealed.
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Jancár J, Slovíková A, Amler E, Krupa P, Kecová H, Plánka L, Gál P, Necas A. Mechanical response of porous scaffolds for cartilage engineering. Physiol Res 2007; 56 Suppl 1:S17-S25. [PMID: 17552899 DOI: 10.33549/physiolres.931297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mechanical properties of scaffolds seeded with mesenchymal stem cells used for cartilage repair seem to be one of the critical factors in possible joint resurfacing. In this paper, the effect of adding hyaluronic acid, hydroxyapatite nanoparticles or chitosan nanofibers into the cross-linked collagen I on the mechanical response of the lyophilized porous scaffold has been investigated in the dry state at 37 oC under tensile loading. Statistical significance of the results was evaluated using ANOVA analysis. The results showed that the addition of hyaluronic acid significantly (p<<0.05) reduced the tensile elastic modulus and enhanced the strength and deformation to failure of the modified cross-linked collagen I under the used test conditions. On the other hand, addition of hydroxyapatite nanoparticles and chitosan nanofibers, respectively, increased the elastic modulus of the modified collagen ten-fold and four-fold, respectively. Hydroxyapatite caused significant reduction in the ultimate deformation at break while chitosan nanofibers enhanced the ultimate deformation under tensile loading substantially (p<<0.05). The ultimate tensile deformation was significantly (p<<0.05) increased by addition of the chitosan nanofibers. The enhanced elastic modulus of the scaffold was translated into enhanced resistance of the porous scaffolds against mechanical load compared to scaffolds based on cross-linked neat collagen or collagen with hyaluronic acid with similar porosity. It can be concluded that enhancing the rigidity of the compact scaffold material by adding rigid chitosan nanofibers can improve the resistance of the porous scaffolds against compressive loading, which can provide more structural protection to the seeded mesenchymal stem cells when the construct is implanted into a lesion. Moreover, scaffolds with chitosan nanofibers seemed to enhance cell growth compared to the neat collagen I when tested in vitro as well as the scaffold stability, extending its resorption to more than 10 weeks.
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53
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Filová E, Rampichová M, Handl M, Lytvynets A, Halouzka R, Usvald D, Hlucilová J, Procházka R, Dezortová M, Rolencová E, Kostáková E, Trc T, Stastný E, Kolácná L, Hájek M, Motlík J, Amler E. Composite hyaluronate-type I collagen-fibrin scaffold in the therapy of osteochondral defects in miniature pigs. Physiol Res 2007; 56 Suppl 1:S5-S16. [PMID: 17552900 DOI: 10.33549/physiolres.931296] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The potential of novel scaffold containing sodium hyaluronate, type I collagen, and fibrin was investigated in the regeneration of osteochondral defects in miniature pigs. Both autologous chondrocyte-seeded scaffolds and non-seeded scaffolds were implanted into two defects located in the non-weight-bearing zone of the femoral trochlea (defect A was located more distally and medially, defect B was located more proximally and laterally). Control defects were left untreated. Twelve weeks after the operation, the knees were evaluated in vivo using MRI. Six months after the implantation, the defects were analyzed using MRI, histological, and immunohistochemical analysis. In the A defects of chondrocyte-seeded scaffold group, hyaline cartilage and fibrocartilage was formed, containing type II collagen, acidic and neutral glycosaminoglycans while the non-seeded scaffold group was predominantly filled with fibrocartilage. Defects in the control group were predominantly filled with fibrous tissue. Histomorphometric analysis of photomicrographs revealed a significantly higher amount of hyaline cartilage in the cell-seeded scaffold group in A defects than in other groups. Both scaffold groups in A defects showed significantly less fibrous tissue than cell-seeded defects B and the control group. Both histological and MRI analysis proved that the novel composite scaffold has a potential to regenerate osteochondral defects within six months.
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Tejral G, Kolácná L, Kotyk A, Amler E. Comparative modeling of the H4-H5-loop of the alpha2-isoform of Na+/K+-ATPase alpha-subunit in the E1 conformation. Physiol Res 2007; 56 Suppl 1:S143-S151. [PMID: 17552883 DOI: 10.33549/physiolres.931313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Restraint-based comparative modeling was used for calculation and visualization of the H4-H5-loop of Na+/K+-ATPase from mouse brain (Mus musculus, adult male brain, alpha2-isoform) between the amino acid residues Cys 336 and Arg 758 in the E1 conformation The structure consists of two well separated parts. The N-domain is formed by a seven-stranded antiparallel beta-sheet with two additional beta-strands and five alpha-helices sandwiching it, the P-domain is composed of a typical Rossman fold. The ATP-binding site was found on the N-domain to be identical in both alpha2- and alpha1-isoforms. The phosphorylation Asp 369 residue was found in the central part of the P-domain, located at the C-terminal end of the central beta-sheet. The distance between the alpha-carbon of Phe 475 at the ATP-binding site and the alpha-carbon of Asp 369 at the phosphorylation site is 3.22 nm. A hydrogen bond between the oxygen atom of Asp 369 and the nitrogen atom of Lys 690 was clearly detected and assumed to play a key role in maintaining the proper structure of the phosphorylaton site in E1 conformation.
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Handl M, Drzík M, Cerulli G, Povýsil C, Chlpík J, Varga F, Amler E, Trc T. Reconstruction of the anterior cruciate ligament: dynamic strain evaluation of the graft. Knee Surg Sports Traumatol Arthrosc 2007; 15:233-41. [PMID: 16972110 DOI: 10.1007/s00167-006-0175-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Accepted: 06/08/2006] [Indexed: 10/24/2022]
Abstract
The study is focused on the biomechanical aspects of the anterior cruciate ligament (ACL) reconstruction procedures with an emphasis on evaluating the dynamic strain of materials commonly used for this purpose. Separate and multiple, equally tensioned strands of hamstring grafts used for the reconstruction of the ACL were biomechanically tested and compared to original ACL and bone-patellar tendon-bone (BPTB) grafts, using tissue samples from cadavers. The study was focused on measuring such material properties as the strength, stiffness, maximum load, and elongation at maximum load of the original ACL, BPTB graft, and single tendon hamstring (gracilis and semitendinosus) grafts, continued by double strands and finally by four-strand graft (STG) evaluation. Fresh-frozen cadaveric knees were used, which had been clamped and tensioned equally. The measurement was performed by drop-weight testing, using a Laser Doppler Vibrometer as a basic sensor of the dynamic movements of the gripping clamps, with parallel correlation by a piezoelectric transducer. The grafts for experiments were obtained from 21-paired knees. The measurement was performed at room temperature (21 degrees C) after 24 h of thawing at 4 degrees C. All the specimens were measured for their response to the dynamic tensile load. The maximum strength values were obtained and calculated for the appropriate section area of the specimen. The tensioned strands of the original ACL showed a maximum average load of 1,246 +/- 243 N in the section area of about 30 mm(2) (max. stress 41.3 MPa); the strands of BPTB grafts showed values of 3,855 +/- 550 N in the section area of 80 mm(2) (max. stress 40.6 MPa); the gracilis tendons showed 925 +/- 127 N in the section area of 10 mm(2) (max. stress 95.1 MPa) and the semitendinosuss yielded a result of 2,050 +/- 159 N in the area of 20 mm(2) (max. stress 88.7 MPa). Of all the materials, the original ACL have the lowest strength and stiffness in respect of their biomechanical properties. BPTB grafts showed a slightly higher value of maximum stress, while both the gracilis and semitendinosus tendons showed double the value of maximum load per section area-tensile stress. Two- and four- combined hamstring strands clamped together and equally tensioned with a drop-weight had the combined tensile strength properties of the individual strands within the estimated range of measurement errors. No significant changes in maximum loads/stresses were observed under impact loading conditions. The results of this study demonstrate that equally tensioned four-strand hamstring-tendon grafts have higher initial tensile properties than those in other varieties of samples. From a biomechanical point of view, they seem to be a reasonable alternative procedure for ACL reconstruction.
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Handl M, Amler E, Bräun K, Holzheu J, Trc T, Imhoff AB, Lytvynets A, Filová E, Kolárová H, Kotyk A, Martínek V. Positive effect of oral supplementation with glycosaminoglycans and antioxidants on the regeneration of osteochondral defects in the knee joint. Physiol Res 2006; 56:243-249. [PMID: 16555950 DOI: 10.33549/physiolres.930917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The effect of oral supplementation with glycosaminoglycans (GAG) and radical scavengers (vitamin E/selenium) on the regeneration of osteochondral defects was investigated in rabbits. After introduction of defined osteochondral defects in the knee joint, groups of ten animals were given a GAG/vitamin E/selenium mixture or a placebo (milk sugar) for 6 weeks. Following sacrifice, histological and histochemical analysis was performed. The amount of synovial fluid was increased in the placebo group, while the viscosity of the synovial fluid was significantly enhanced in the GAG group. The amount of sulfated GAG in the osteochondral regenerates (8.8 +/- 3.6 % vs. 6.0 +/- 5.6 %; p <0.03) was significantly higher in the GAG group. In both groups, the GAG amount in the cartilage of the operated knee was significantly higher than in the non-involved knee (p <0.05). Histological analysis of the regenerates in the GAG group was superior in comparison with the placebo group. For the first time, a biological effect following oral supplementation with GAG was demonstrated in healing of osteochondral defects in vivo. These findings support the known positive clinical results.
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57
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Handl M, Filová E, Kubala M, Lánský Z, Kolácná L, Vorlícek J, Trc T, Pach M, Amler E. Fluorescent advanced glycation end products in the detection of factual stages of cartilage degeneration. Physiol Res 2006; 56:235-242. [PMID: 16555949 DOI: 10.33549/physiolres.930934] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Patients treated for knee disorders were included in this study. They were examined clinically (Lequesne and Tegner scores) and by standard X-ray investigation. Patients underwent a surgical procedure, either arthroscopy or knee replacement. At the initial phase of surgery, a sample of cartilage was taken for laboratory examination. Progression of the disorder and the clinical examination was correlated with the actual state of the cartilage using a novel fluorescence approach. The intrinsic fluorescence of cartilages was shown as a suitable and sensitive method for detection of the actual state of cartilages because the correlation with X-ray examination and clinical status was found. Intrinsic fluorescence properties of cartilages from patients with chondropathy and osteoarthritis were described and found to be age-dependent. We also observed a higher concentration of advanced glycation end products due to inflammatory and/or degenerative processes in the cartilage. In addition, acute pathological changes due to diseases such as meniscal lesions or anterior cruciate ligament rupture caused a significant increase of formation of advanced glycation end products even in the group of young patients. In fact, such an observation could be crucial and important for the detection of knee conditions suspected of early meniscal and/or ACL lesions especially among young patients.
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MESH Headings
- Adolescent
- Adult
- Age Distribution
- Age Factors
- Aged
- Aged, 80 and over
- Arthroplasty, Replacement, Knee
- Arthroscopy
- Cartilage Diseases/diagnosis
- Cartilage Diseases/diagnostic imaging
- Cartilage Diseases/metabolism
- Cartilage Diseases/surgery
- Cartilage, Articular/diagnostic imaging
- Cartilage, Articular/metabolism
- Cartilage, Articular/surgery
- Female
- Glycation End Products, Advanced/metabolism
- Humans
- Joint Diseases/diagnosis
- Joint Diseases/diagnostic imaging
- Joint Diseases/metabolism
- Joint Diseases/surgery
- Knee Injuries/diagnosis
- Knee Injuries/diagnostic imaging
- Knee Injuries/metabolism
- Knee Injuries/surgery
- Knee Joint/diagnostic imaging
- Knee Joint/metabolism
- Knee Joint/surgery
- Male
- Middle Aged
- Osteoarthritis, Knee/diagnosis
- Osteoarthritis, Knee/metabolism
- Predictive Value of Tests
- Radiography
- Sensitivity and Specificity
- Severity of Illness Index
- Spectrometry, Fluorescence
- Synovitis/diagnosis
- Synovitis/metabolism
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58
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Varga F, Držik M, Handl M, Chlpik J, Filová E, Amler E. Experimental evaluation of biological samples impact response. J Biomech 2006. [DOI: 10.1016/s0021-9290(06)85032-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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59
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Lansky Z, Kubala M, Varga F, Kolacna L, Amler E. Protein structure and dynamics determined by protein modeling combined with spectroscopic techniques. BRATISL MED J 2006; 107:118-22. [PMID: 16796138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Beside of the protein crystals, another attractive option in protein structure analysis has recently appeared: computer modeling of the protein structure based on homology and similarity with proteins of already known structures. We used the combination of computer modeling with spectroscopic techniques, such as steady-state or time-resolved fluorescence spectroscopy or Raman spectroscopy, and with molecular biology techniques. This method could achieve reliable results comparable with resolution obtained from crystal structures. Molecular modeling of the ATP site within the H4-H5-loop revealed eight amino acids residues, namely besides the previously reported amino acids Asp443, Lys480, Lys501, Gly502 and Arg544, also Glu446, Phe475 and Gln482, which form the complete ATP recognition site. Moreover, we proved that a hydrogen bond between Arg423 and Glu472 supported the connection of two opposite halves of the ATP-binding pocket. Similarly, the conserved residue Pro489 is important for the proper interaction of the third and fourth-strands, which both contain residues that take part in the ATP-binding (Ref. 34).
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60
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Konopásek I, Vecer J, Strzalka K, Amler E. Short-lived fluorescence component of DPH reports on lipid--water interface of biological membranes. Chem Phys Lipids 2005; 130:135-44. [PMID: 15172830 DOI: 10.1016/j.chemphyslip.2004.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2003] [Revised: 02/06/2004] [Accepted: 02/19/2004] [Indexed: 10/26/2022]
Abstract
Fluorescence measurements of 1,6-diphenyl-1,3,5-hexatriene (DPH) in large unilamellar phospholipid vesicles were performed to characterize the influence of the membrane physical properties on the short-lived lifetime component of the fluorescence decay. We have found that the short-lived component of DPH significantly shortens when the membrane undergoes a temperature-induced phase transition as it is known for the long-lived component of DPH. We induced membrane phase transitions also by alcohols, which are reported to be distributed different way in the membrane--ethanol close to the membrane-water interface and benzyl alcohol in the membrane core. A different effect of the respective alcohol on the short and long decay component was observed. Both the time-resolved fluorescence spectra of DPH taken during lipid vesicle staining and the lifetime dependences caused by changes of temperature and/or induced by the alcohols show that the short-lived fluorescence originates from the population of dye molecules distributed at the membrane-water interface.
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61
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Krumscheid R, Ettrich R, Sovová Z, Susánková K, Lánský Z, Hofbauerová K, Linnertz H, Teisinger J, Amler E, Schoner W. The phosphatase activity of the isolated H4-H5 loop of Na+/K+ ATPase resides outside its ATP binding site. ACTA ACUST UNITED AC 2004; 271:3923-36. [PMID: 15373838 DOI: 10.1111/j.1432-1033.2004.04330.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural stability of the large cytoplasmic domain (H(4)-H(5) loop) of mouse alpha(1) subunit of Na(+)/K(+) ATPase (L354-I777), the number and the location of its binding sites for 2'-3'-O-(trinitrophenyl) adenosine 5'-triphosphate (TNP-ATP) and p-nitrophenylphosphate (pNPP) were investigated. C- and N-terminal shortening revealed that neither part of the phosphorylation (P)-domain are necessary for TNP-ATP binding. There is no indication of a second ATP site on the P-domain of the isolated loop, even though others reported previously of its existence by TNP-N(3)ADP affinity labeling of the full enzyme. Fluorescein isothiocyanate (FITC)-anisotropy measurements reveal a considerable stability of the nucleotide (N)-domain suggesting that it may not undergo a substantial conformational change upon ATP binding. The FITC modified loop showed only slightly diminished phosphatase activity, most likely due to a pNPP site on the N-domain around N398 whose mutation to D reduced the phosphatase activity by 50%. The amino acids forming this pNPP site (M384, L414, W411, S400, S408) are conserved in the alpha(1-4) isoforms of Na(+)/K(+) ATPase, whereas N398 is only conserved in the vertebrates' alpha(1) subunit. The phosphatase activity of the isolated H(4)-H(5) loop was neither inhibited by ATP, nor affected by mutation of D369, which is phosphorylated in native Na(+)/K(+) ATPase.
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62
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Lánský Z, Kubala M, Ettrich R, Kutý M, Plásek J, Teisinger J, Schoner W, Amler E. The hydrogen bonds between Arg423 and Glu472 and other key residues, Asp443, Ser477, and Pro489, are responsible for the formation and a different positioning of TNP-ATP and ATP within the nucleotide-binding site of Na(+)/K(+)-ATPase. Biochemistry 2004; 43:8303-11. [PMID: 15222743 DOI: 10.1021/bi0496485] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutation of Arg(423) at the N-domain of Na(+)/K(+)-ATPase resulted in a large decrease of both TNP-ATP and ATP binding. Thus, this residue, localized outside the binding pocket, seems to play a key role in supporting the proper structure and shape of the binding site. In addition, mutation of Glu(472) also caused a large decrease of both TNP-ATP and ATP binding. On the basis of our computer model, we hypothesized that a hydrogen bond between Arg(423) and Glu(472) supports the connection of two opposite halves of the ATP-binding pocket. To verify this hypothesis, we have also prepared the construct containing both these mutations. Binding of neither TNP-ATP nor ATP to this double mutant differed from binding to any of the single mutants. This strongly supported the existence of the hydrogen bond between Arg(423) and Glu(472). Similarly, the conserved residue Pro(489) seems to be substantial for the proper interaction of the third and fourth beta-strands of the N-domain, which both contain residues that take part in ATP binding. Mutation of Asp(443) affected only ATP, but not TNP-ATP, binding, suggesting that these ligands adopt different positions in the nucleotide-binding pocket. On the basis of a recently published crystal structure [Håkansson, K. O. (2003) J. Mol. Biol. 332, 1175-1182], we improved our model and computed the interaction of these two ligands with the N-domain. This model is in good agreement with all previously reported spectroscopic data and revealed that Asp(443) forms a hydrogen bond with the NH(2) group of the adenosine moiety of ATP, but not TNP-ATP.
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63
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Janata J, Holá K, Kubala M, Gakh O, Parkhomenko N, Matusková A, Kutejová E, Amler E. Substrate evokes translocation of both domains in the mitochondrial processing peptidase alpha-subunit during which the C-terminus acts as a stabilizing element. Biochem Biophys Res Commun 2004; 316:211-7. [PMID: 15003532 DOI: 10.1016/j.bbrc.2004.02.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2004] [Indexed: 11/22/2022]
Abstract
All three tryptophan residues in alpha-subunit of mitochondrial processing peptidase (MPP) were subsequently substituted. While substitutions of Trp223 led to misfolded non-functional protein, mutations of Trp147 and/or Trp481 did not affect the enzyme processing activity. Thus, fluorescence properties of the mutants with fewer tryptophans were used for observation of both alpha-MPP domain translocation and visualization of conformational changes in the interdomain linker evoked by substrate. We found that in the presence of substrate the C-terminal penultimate Trp481 was approaching Trp223, which is localized at the border of N-terminal domain and interdomain linker. Also, excision of the alpha-MPP C-terminal 30 amino acid residues (DeltaC30) led to a complete loss of protein function. Even shorter deletions of the alpha-MPP C-terminus destabilized the protein slightly (DeltaC2) or dramatically (DeltaC17). It suggests that the extreme C-terminus of alpha-MPP provides mechanical support to the C-terminal domain during its extensive conformational change accompanying the substrate recognition process.
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64
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Kubala M, Plášek J, Amler E. Fluorescence Competition Assay for the Assessment of ATP Binding to an Isolated Domain of Na+, K+-ATPase. Physiol Res 2004. [DOI: 10.33549/physiolres.930394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
An equation allowing estimation of the dissociation constant for binding of a non-fluorescent ligand to the enzyme is presented that is based on the competitive replacement of the ligand by its fluorescent analog. We derived an explicit formula for the probe fluorescence intensity, which is suitable for nonlinear least-squares analysis. We used this formula to evaluate the binding of ATP to the large cytoplasmic loop of Na+,K(+)-ATPase. The estimated value of KD (6.2+/- 0.7 mM) is comparable with the results from other laboratories for similar constructs obtained by a different method.
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65
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Kubala M, Plásek J, Amler E. Fluorescence competition assay for the assessment of ATP binding to an isolated domain of Na+, K(+)-ATPase. Physiol Res 2004; 53:109-13. [PMID: 14984322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
An equation allowing estimation of the dissociation constant for binding of a non-fluorescent ligand to the enzyme is presented that is based on the competitive replacement of the ligand by its fluorescent analog. We derived an explicit formula for the probe fluorescence intensity, which is suitable for nonlinear least-squares analysis. We used this formula to evaluate the binding of ATP to the large cytoplasmic loop of Na+,K(+)-ATPase. The estimated value of KD (6.2+/- 0.7 mM) is comparable with the results from other laboratories for similar constructs obtained by a different method.
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66
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Kubala M, Obsil T, Obsilová V, Lánský Z, Amler E. Protein modeling combined with spectroscopic techniques: an attractive quick alternative to obtain structural information. Physiol Res 2004; 53 Suppl 1:S187-97. [PMID: 15119949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Beside of the protein crystallography or NMR, another attractive option in protein structure analysis has recently appeared: computer modeling of the protein structure based on homology and similarity with proteins of already known structures. We have used the combination of computer modeling with spectroscopic techniques, such as steady-state or time-resolved fluorescence spectroscopy, and with molecular biology techniques. This method could provide useful structural information in the cases where crystal or NMR structure is not available. Molecular modeling of the ATP site within the H4-H5-loop revealed eight amino acids residues, namely besides the previously reported amino acids Asp443, Lys480, Lys501, Gly502 and Arg544, also Glu446, Phe475 and Gln482, which form the complete ATP recognition site. Moreover, we have proved that a hydrogen bond between Arg423 and Glu472 supports the connection of two opposite halves of the ATP-binding pocket. Similarly, the conserved residue Pro489 is important for the proper interaction of the third and fourth beta-strands, which both contain residues that take part in the ATP-binding. Alternatively, molecular dynamics simulation combined with dynamic fluorescence spectroscopy revealed that 14-3-3 zeta C-terminal stretch is directly involved in the interaction of 14-3-3 protein with the ligand. Phosphorylation at Thr232 induces a conformational change of the C-terminus, which is presumably responsible for observed inhibition of binding abilities. Phosphorylation at Thr232 induces more extended conformation of 14-3-3zeta C-terminal stretch and changes its interaction with the rest of the 14-3-3 molecule. This could explain negative regulatory effect of phosphorylation at Thr232 on 14-3-3 binding properties.
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67
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Kubala M, Plásek J, Amler E. Limitations in linearized analyses of binding equilibria: binding of TNP-ATP to the H4-H5 loop of Na/K-ATPase. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2003; 32:363-9. [PMID: 12851794 DOI: 10.1007/s00249-003-0278-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2002] [Revised: 11/28/2002] [Accepted: 12/05/2002] [Indexed: 11/26/2022]
Abstract
Binding of TNP-ATP [2',3'- O-(2,4,6-trinitrophenyl)adenosine 5'-triphosphate, a fluorescent analogue of ATP] to the K605 protein was studied. This is an isolated N-domain in the cytoplasmic loop of the Na/K-ATPase alpha-subunit, lying between membrane-spanning segments 4 and 5 (sequence L(354)-I(604)). A titration equation is derived that explicitly makes it possible to relate the fluorescence of TNP-ATP and K605 solutions to total probe concentration in the sample. Using this, it is possible to obtain the value of the dissociation constant from the titration experiment without resorting to the Scatchard plot, which is far from optimal from the statistical point of view. Using the new formula with non-linear regression analysis, a value of the dissociation constant K(D) for TNP-ATP binding to the K605 protein of 3.03 +/- 0.28 microM at 22 degrees C was obtained. A series of fits to simulated data with added noise demonstrated clearly the advantage of non-linear regression using the new formula over the commonly employed linear regression using the Scatchard plot. The procedure presented is generally applicable to binding assays using changes in the fluorescence of ligands on binding.
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68
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Hofbauerová K, Kopecký V, Ettrich R, Kubala M, Teisinger J, Amler E. ATP-binding is stabilized by a stacking interaction within the binding site of Na+/K+ -ATPase. Biochem Biophys Res Commun 2003; 306:416-20. [PMID: 12804579 DOI: 10.1016/s0006-291x(03)00946-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Site-directed mutagenesis was applied to modify phenylalanines (Phe(475)Trp, Phe(548)Tyr, and both) to generate mutants on the basis of molecular modeling of the ATP-binding domain of Na(+)/K(+)-ATPase, in order to characterize the forces that stabilize ATP in its binding pocket. Each of the mutants was examined by Raman difference spectroscopy, i.e., as a difference between the spectrum of the domain with and without bound ATP. It was shown that Phe(475) plays a key role in stabilizing ATP-binding by a stacking interaction. Phe(548) co-stabilizes ATP on the opposite site of the binding pocket and its type of interaction with ATP-binding differs from that of Phe(475).
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Kubala M, Teisinger J, Ettrich R, Hofbauerová K, Kopecký V, Baumruk V, Krumscheid R, Plásek J, Schoner W, Amler E. Eight amino acids form the ATP recognition site of Na(+)/K(+)-ATPase. Biochemistry 2003; 42:6446-52. [PMID: 12767226 DOI: 10.1021/bi034162u] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Point mutations of a part of the H(4)-H(5) loop (Leu(354)-Ile(604)) of Na(+)/K(+)-ATPase have been used to study the ATP and TNP-ATP binding affinities. Besides the previously reported amino acid residues Lys(480), Lys(501), Gly(502), and Cys(549), we have found four more amino acid residues, viz., Glu(446), Phe(475), Gln(482), and Phe(548), completing the ATP-binding pocket of Na(+)/K(+)-ATPase. Moreover, mutation of Arg(423) has also resulted in a large decrease in the extent of ATP binding. This residue, localized outside the binding pocket, seems to play a key role in supporting the proper structure and shape of the binding site, probably due to formation of a hydrogen bond with Glu(472). On the other hand, only some minor effects were caused by mutations of Ile(417), Asn(422), Ser(445), and Glu(505).
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Gregor M, Kubala M, Amler E, Mejsnar J. Frequency-domain lifetime fluorometry of double-labeled creatine kinase. Physiol Res 2003; 52:579-85. [PMID: 14535833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
Myofibril-bound creatine kinase EC 2.7.3.2 (CK), a key enzyme of muscle energy metabolism, has been selected for studies of conformational changes that underlie the cellular control of enzyme activity. For fluorescence spectroscopy measurements, the CK molecule was double-labeled with IAF (5-iodoacetamidofluorescein) and ErITC (erythrosin 5'-isothiocyanate). Measurement of fluorescence resonance energy transfer (FRET) from fluorescein to erythrosin was used to obtain information about the donor-acceptor pair distance. Frequency-domain lifetime measurements evaluate the donor-acceptor distance in the native CK molecule as 7.8 nm. The Förster radius equals 5.3 nm with the resolution range from 0.2 to 1.0 nm. Erythrosin-fluorescein labeling (EFL) was tested for artificial conformational changes of the CK molecule with high-salt concentration treatment. The transition distance, defined by His-97 and Cys-283 and derived from a 3D model equals 0.766 nm for the open (inactive) form and 0.277 nm for the closed (reactive) form of the CK molecule. In this way, the resolution range of the used spectroscopy method is significant, concerning the difference of 0.489 nm. Nevertheless, the CK enzyme activity, assessed by the hexokinase-coupled assay, was diminished down to 1 % of the activity of the native enzyme. EFL is suitable for description of conformational behavior implied from the regulation of creatine kinase. However, the observed inhibition restricts EFL to studies of conformational changes during natural catalytic activity.
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Kubala M, Hofbauerová K, Ettrich R, Kopecký V, Krumscheid R, Plásek J, Teisinger J, Schoner W, Amler E. Phe(475) and Glu(446) but not Ser(445) participate in ATP-binding to the alpha-subunit of Na(+)/K(+)-ATPase. Biochem Biophys Res Commun 2002; 297:154-9. [PMID: 12220524 DOI: 10.1016/s0006-291x(02)02089-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The ATP-binding site of Na(+)/K(+)-ATPase is localized on the large cytoplasmic loop of the alpha-subunit between transmembrane helices H(4) and H(5). Site-directed mutagenesis was performed to identify residues involved in ATP binding. On the basis of our recently developed model of this loop, Ser(445), Glu(446), and Phe(475) were proposed to be close to the binding pocket. Replacement of Phe(475) with Trp and Glu(446) with Gln profoundly reduced the binding of ATP, whereas the substitution of Ser(445) with Ala did not affect ATP binding. Fluorescence measurements of the fluorescent analog TNP-ATP, however, indicated that Ser(445) is close to the binding site, although it does not participate in binding.
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Hofbauerová K, Kopecký V, Ettrich R, Ettrichová O, Amler E. Secondary and tertiary structure of nucleotide-binding domain of alphasubunit of Na+/K+-ATPase. Biopolymers 2002; 67:242-6. [PMID: 12012438 DOI: 10.1002/bip.10093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nucleotide-binding domain of the alpha subunit of mouse brain Na+/K+-ATPase was expressed and isolated from Escherichia coli cells. A model structure was constructed by comparative modeling with and without docked ATP. This was compared with the secondary structure determination from UV circular dichroism and Raman spectroscopy. Thus, we support the quality of the model and the correct folding of the recombinant protein. ATP binding was followed by Raman difference spectroscopy, and its influence on the secondary structure of the N domain seems to not be significant.
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Teisinger J, Hofbauerova K, Kvasnicka P, Schoner W, Amler E, Ettrich R, Melichercik M, Krumscheid R, Ettrichova O. Three-dimensional structure of the large cytoplasmic H 4 ?H 5 loop of Na + /K + -ATPase deduced by restraint-based comparative modeling shows only one ATP binding site. J Mol Model 2001. [DOI: 10.1007/s008940100031] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gakh O, Obsil T, Adamec J, Spizek J, Amler E, Janata J, Kalousek F. Substrate binding changes conformation of the alpha-, but not the beta-subunit of mitochondrial processing peptidase. Arch Biochem Biophys 2001; 385:392-6. [PMID: 11368022 DOI: 10.1006/abbi.2000.2167] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lifetime analysis of tryptophan fluorescence of the mitochondrial processing peptidase (MPP) from Saccharomyces cerevisiae clearly proved that substrate binding evoked a conformational change of the alpha-subunit while presence of substrate influenced neither the lifetime components nor the average lifetime of the tryptophan excited state of the beta-MPP subunit. Interestingly, lifetime analysis of tryptophan fluorescence decay of the alpha-MPP subunit revealed about 11% of steady-state fractional intensity due to the long-lived lifetime component, indicating that at least one tryptophan residue is partly buried at the hydrophobic microenvironment. Computer modeling, however, predicted none of three tryptophans, which the alpha-subunit contains, as deeply buried in the protein matrix. We conclude this as a consequence of a possible dimeric (oligomeric) structure.
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Tanfani F, Linnertz H, Obsil T, Krumscheid R, Urbanova P, Jelinek O, Mazzanti L, Bertoli E, Schoner W, Amler E. Effects of fluorescent pseudo-ATP and ATP-metal analogs on secondary structure of Na(+)/K(+)-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1457:94-102. [PMID: 10692553 DOI: 10.1016/s0005-2728(00)00055-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The secondary structure of Na(+)/K(+)-ATPase after modification of the ATP-binding sites was analyzed. Consistently with recent reports, we found in trypsin-treated Na(+)/K(+)-ATPase additionally to alpha-helix also beta-sheet structures in the transmembrane segments. However, binding of fluorescein 5'-isothiocyanate (FITC), the pseudo-ATP analog, to the ATP-binding site did not affect the secondary structure of undigested Na(+)/K(+)-ATPase. Consequently, fluorescence intensity changes of FITC-labeled Na(+)/K(+)-ATPase commonly used to observe conformational transitions of the enzyme reflect physiological changes of the native structure. The metal complex analogues of ATP, Cr(H(2)O)(4)ATP and Co(NH(3))(4)ATP, on the other hand, affected the secondary structure of Na(+)/K(+)-ATPase. We propose that these changes in the secondary structure are responsible for inhibition of backdoor phosphorylation.
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