Macroscopic cartilage repair scoring of defect fill, integration and total points correlate with corresponding items in histological scoring systems - a study in adult sheep

OBJECTIVE

To correlate osteochondral repair assessed by validated macroscopic scoring systems with established semiquantitative histological analyses in an ovine model and to test the hypothesis that important macroscopic individual categories correlate with their corresponding histological counterparts.

METHODS

In the weight-bearing portion of medial femoral condyles (n = 38) of 19 female adult Merino sheep (age 2-4 years; weight 70 ± 20 kg) full-thickness chondral defects were created (size 4 × 8 mm; International Cartilage Repair Society (ICRS) grade 3C) and treated with Pridie drilling. After sacrifice, 1520 blinded macroscopic observations from three observers at 2-3 time points including five different macroscopic scoring systems demonstrating all grades of cartilage repair where correlated with corresponding categories from 418 blinded histological sections.

RESULTS

Categories "defect fill" and "total points" of different macroscopic scoring systems correlated well with their histological counterparts from the Wakitani and Sellers scores (all P ≤ 0.001). "Integration" was assessed in both histological scoring systems and in the macroscopic ICRS, Oswestry and Jung scores. Here, a significant relationship always existed (0.020 ≤ P ≤ 0.049), except for Wakitani and Oswestry (P = 0.054). No relationship was observed for the "surface" between histology and macroscopy (all P > 0.05).

CONCLUSIONS

Major individual morphological categories "defect fill" and "integration", and "total points" of macroscopic scoring systems correlate with their corresponding categories in elementary and complex histological scoring systems. Thus, macroscopy allows to precisely predict key histological aspects of articular cartilage repair, underlining the specific value of macroscopic scoring for examining cartilage repair.

[Patella position and patellofemoral osteoarthritis after unicompartmental arthroplasty]

BACKGROUND

Changes of patellar position (height, tilt, and shift) and arthritis of the patellofemoral joint might potentially influence outcome after unicompartmental knee replacement.

OBJECTIVES

The purpose of this work is to evaluate the influence of the aforementioned parameters on postoperative outcome.

METHODS

Literature analysis via PubMed.

RESULTS

A total of 12 relevant studies (three about Patellar height, two about patellar tilt and shift, seven about patellofemoral osteoarthritis) could be identified. Regarding Patellar height, two out of three studies demonstrated a postoperative decrease. With regard to patellar tilt and shift, only one study identified postoperative lateralization of the patella to be a predictor for poor outcome. The radiological appearance of arthritis of the patellofemoral joint does not significantly influence postoperative knee function except for cases where only the lateral patellar facet is affected. Anterior knee pain has no influence on clinical outcome.

CONCLUSION

Literature data do not allow for a precise statement about the possible influence of patellar position on the outcome after unicompartmental knee replacement. With proper patient selection, good results can be achieved despite patellofemoral osteoarthritis.

PTH [1-34]-induced alterations of the subchondral bone provoke early osteoarthritis

OBJECTIVE

To test the hypothesis that changes in the subchondral bone induced by parathyroid hormone (PTH [1-34]) reciprocally affect the integrity of the articular cartilage within a naïve osteochondral unit in vivo.

DESIGN

Daily subcutaneous injections of 10 μg PTH [1-34]/kg were given to adult rabbits for 6 weeks, controls received saline. Blood samples were continuously collected to monitor renal function. The subchondral bone plate and subarticular spongiosa of the femoral heads were separately assessed by micro-computed tomography. Articular cartilage was evaluated by macroscopic and histological osteoarthritis scoring, polarized light microscopy, and immunohistochemical determination of type-I, type-II, type-X collagen contents, PTH [1-34] receptor and caspase-3 expression. Absolute and relative extents of hyaline and calcified articular cartilage layers were measured histomorphometrically. The correlation between PTH-induced changes in subchondral bone and articular cartilage was determined.

RESULTS

PTH [1-34] enhanced volume, mineral density, and trabecular thickness within the subarticular spongiosa, and increased thickness of the calcified cartilage layer (all P < 0.05). Moreover, PTH [1-34] led to cartilage surface irregularities and reduced matrix staining (both P < 0.03). These early osteoarthritic changes correlated with and were ascribed to the increased thickness of the calcified cartilage layer (P = 0.026) and enhanced mineral density of the subarticular spongiosa (P = 0.001).

CONCLUSIONS

Modifications of the subarticular spongiosa by PTH [1-34] cause broadening of the calcified cartilage layer, resulting in osteoarthritic cartilage degeneration. These findings identify a mechanism by which PTH-induced alterations of the normal subchondral bone microarchitecture may provoke early osteoarthritis.

Alterations of the subchondral bone in osteochondral repair--translational data and clinical evidence

Alterations of the subchondral bone are pathological features associated with spontaneous osteochondral repair following an acute injury and with articular cartilage repair procedures. The aim of this review is to discuss their incidence, extent and relevance, focusing on recent knowledge gained from both translational models and clinical studies of articular cartilage repair. Efforts to unravel the complexity of subchondral bone alterations have identified (1) the upward migration of the subchondral bone plate, (2) the formation of intralesional osteophytes, (3) the appearance of subchondral bone cysts, and (4) the impairment of the osseous microarchitecture as potential problems. Their incidence and extent varies among the different small and large animal models of cartilage repair, operative principles, and over time. When placed in the context of recent clinical investigations, these deteriorations of the subchondral bone likely are an additional, previously underestimated, factor that influences the long-term outcome of cartilage repair strategies. Understanding the role of the subchondral bone in both experimental and clinical articular cartilage repair thus holds great promise of being translated into further improved cell- or biomaterial-based techniques to preserve and restore the entire osteochondral unit.

Parathyroid hormone [1-34] improves articular cartilage surface architecture and integration and subchondral bone reconstitution in osteochondral defects in vivo

OBJECTIVE

The 1-34 amino acid segment of the parathyroid hormone (PTH [1-34]) mediates anabolic effects in chondrocytes and osteocytes. The aim of this study was to investigate whether systemic application of PTH [1-34] improves the repair of non-osteoarthritic, focal osteochondral defects in vivo.

DESIGN

Standardized cylindrical osteochondral defects were bilaterally created in the femoral trochlea of rabbits (n = 8). Daily subcutaneous injections of 10 μg PTH [1-34]/kg were given to the treatment group (n = 4) for 6 weeks, controls (n = 4) received saline. Articular cartilage repair was evaluated by macroscopic, biochemical, histological and immunohistochemical analyses. Reconstitution of the subchondral bone was assessed by micro-computed tomography. Effects of PTH [1-34] on synovial membrane, apoptosis, and expression of the PTH receptor (PTH1R) were determined.

RESULTS

Systemic PTH [1-34] increased PTH1R expression on both, chondrocytes and osteocytes within the repair tissue. PTH [1-34] ameliorated the macro- and microscopic aspect of the cartilaginous repair tissue. It also enhanced the thickness of the subchondral bone plate and the microarchitecture of the subarticular spongiosa within the defects. No significant correlations were established between these coexistent processes. Apoptotic levels, synovial membrane, biochemical composition of the repair tissue, and type-I/II collagen immunoreactivity remained unaffected.

CONCLUSIONS

PTH [1-34] emerges as a promising agent in the treatment of focal osteochondral defects as its systemic administration simultaneously stimulates articular cartilage and subchondral bone repair. Importantly, both time-dependent mechanisms of repair did not correlate significantly at this early time point and need to be followed over prolonged observation periods.

Temporal and spatial migration pattern of the subchondral bone plate in a rabbit osteochondral defect model

OBJECTIVE

Upward migration of the subchondral bone plate is associated with osteochondral repair. The aim of this study was to quantitatively monitor the sequence of subchondral bone plate advancement in a lapine model of spontaneous osteochondral repair over a 1-year period and to correlate these findings with articular cartilage repair.

DESIGN

Standardized cylindrical osteochondral defects were created in the rabbit trochlear groove. Subchondral bone reconstitution patterns were identified at five time points. Migration of the subchondral bone plate and areas occupied by osseous repair tissue were determined by histomorphometrical analysis. Tidemark formation and overall cartilage repair were correlated with the histomorphometrical parameters of the subchondral bone.

RESULTS

The subchondral bone reconstitution pattern was cylindrical at 3 weeks, infundibuliform at 6 weeks, plane at 4 and 6 months, and hypertrophic after 1 year. At this late time point, the osteochondral junction advanced 0.19 [95% confidence intervals (CI) 0.10-0.30] mm above its original level. Overall articular cartilage repair was significantly improved by 4 and 6 months but degraded after 1 year. Subchondral bone plate migration correlated with tidemark formation (r = 0.47; P < 0.0001), but not with the overall score of the repair cartilage (r = 0.11; P > 0.44).

CONCLUSIONS

The subchondral bone plate is reconstituted in a distinct chronological order. The lack of correlation suggests that articular cartilage repair and subchondral bone reconstitution proceed at a different pace and that the advancement of the subchondral bone plate is not responsible for the diminished articular cartilage repair in this model.

Experimental scoring systems for macroscopic articular cartilage repair correlate with the MOCART score assessed by a high-field MRI at 9.4 T--comparative evaluation of five macroscopic scoring systems in a large animal cartilage defect model

OBJECTIVE

To develop a new macroscopic scoring system which allows for an overall judgment of experimental articular cartilage repair and compare it with four existing scoring systems and high-field magnetic resonance imaging (MRI).

METHODS

A new macroscopic scoring system was developed to assess the repair of cartilage defects. Cartilage repair was graded by three observers with different experience in cartilage research at 2-3 time points and compared with the protocol A of the international cartilage repair society (ICRS) cartilage repair assessment score, the Oswestry arthroscopy score, and macroscopic grading systems designed by Jung and O'Driscoll. Parameters were correlated with the two-dimensional (2D) magnetic resonance observation of cartilage repair tissue (MOCART) score based on a 9.4 T MRI as an external reference standard.

RESULTS

All macroscopic scores exhibited high intra- and interobserver reliability and high internal correlation. The newly developed macroscopic scoring system had the highest intraobserver [0.866 ≤ intraclass correlation (ICC) ≤ 0.895] and the highest interobserver reliability (ICC = 0.905) for "total points". Here, Cronbach's alpha indicated good homogeneity and functioning of the items (mean = 0.782). "Total points" of the 2D MOCART score correlated with all macroscopic scores (all P < 0.0001). The newly developed macroscopic scoring system yielded the highest correlation for the MRI parameter "defect fill" (rho = 0.765; all P < 0.0001).

CONCLUSIONS

"Total points" and "defect fill", two clinically relevant indicators of cartilage repair, can be reliably and directly assessed by macroscopic evaluation, using either system. These data support the use of macroscopic assessment to precisely judge cartilage repair in preclinical large animal models.

Crystal structure of omega transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 A resolution

The 71 amino acid residue omega protein encoded by the Streptococcus pyogenes non-conjugative plasmid pSM19035 is a transcriptional repressor that regulates expression of genes for copy number control and stable maintenance of plasmids. The crystal structure of omega protein has been determined by multiple isomorphous replacement, including anomalous scattering and refined to an R-factor of 21.1 % (R(free)=23.2 %) at 1.5 A resolution. Two monomers related by a non-crystallographic 2-fold axis form a homodimer that occupies the asymmetric unit. Each polypeptide chain is folded into two alpha-helices and one beta-strand forming an antiparallel beta-ribbon in the homodimer. The N-terminal regions (1-23 and 1-22 in subunits I and II, respectively) are not defined in the electron density due to proteolysis of the N-terminal 20 amino acid residues during crystallisation and partial disorder. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognizing the major groove of operator DNA; according to a modelled omega protein-DNA complex, residues Arg31 and Arg31' on the beta-ribbon are in positions to interact with a nucleobase, especially guanine.

Excited-state dynamics in photosystem II: insights from the x-ray crystal structure

The heart of oxygenic photosynthesis is photosystem II (PSII), a multisubunit protein complex that uses solar energy to drive the splitting of water and production of molecular oxygen. The effectiveness of the photochemical reaction center of PSII depends on the efficient transfer of excitation energy from the surrounding antenna chlorophylls. A kinetic model for PSII, based on the x-ray crystal structure coordinates of 37 antenna and reaction center pigment molecules, allows us to map the major energy transfer routes from the antenna chlorophylls to the reaction center chromophores. The model shows that energy transfer to the reaction center is slow compared with the rate of primary electron transport and depends on a few bridging chlorophyll molecules. This unexpected energetic isolation of the reaction center in PSII is similar to that found in the bacterial photosystem, conflicts with the established view of the photophysics of PSII, and may be a functional requirement for primary photochemistry in photosynthesis. In addition, the model predicts a value for the intrinsic photochemical rate constant that is 4 times that found in bacterial reaction centers.

Photosystem II single crystals studied by EPR spectroscopy at 94 GHz: the tyrosine radical Y(D)(*)

Electron paramagnetic resonance (EPR) spectroscopy at 94 GHz is used to study the dark-stable tyrosine radical Y(D)(*) in single crystals of photosystem II core complexes (cc) isolated from the thermophilic cyanobacterium Synechococcus elongatus. These complexes contain at least 17 subunits, including the water-oxidizing complex (WOC), and 32 chlorophyll a molecules/PS II; they are active in light-induced electron transfer and water oxidation. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with four PS II dimers per unit cell. High-frequency EPR is used for enhancing the sensitivity of experiments performed on small single crystals as well as for increasing the spectral resolution of the g tensor components and of the different crystal sites. Magnitude and orientation of the g tensor of Y(D)(*) and related information on several proton hyperfine tensors are deduced from analysis of angular-dependent EPR spectra. The precise orientation of tyrosine Y(D)(*) in PS II is obtained as a first step in the EPR characterization of paramagnetic species in these single crystals.

Crystal structure of photosystem II from Synechococcus elongatus at 3.8 A resolution

Oxygenic photosynthesis is the principal energy converter on earth. It is driven by photosystems I and II, two large protein-cofactor complexes located in the thylakoid membrane and acting in series. In photosystem II, water is oxidized; this event provides the overall process with the necessary electrons and protons, and the atmosphere with oxygen. To date, structural information on the architecture of the complex has been provided by electron microscopy of intact, active photosystem II at 15-30 A resolution, and by electron crystallography on two-dimensional crystals of D1-D2-CP47 photosystem II fragments without water oxidizing activity at 8 A resolution. Here we describe the X-ray structure of photosystem II on the basis of crystals fully active in water oxidation. The structure shows how protein subunits and cofactors are spatially organized. The larger subunits are assigned and the locations and orientations of the cofactors are defined. We also provide new information on the position, size and shape of the manganese cluster, which catalyzes water oxidation.

A direct photo-activated affinity modification of tetracycline transcription repressor protein TetR(D) with tetracycline(1)

Results of a first successful application of a direct photo-induced affinity modification of Tet repressor (TetR(D)) protein with tetracycline within a complex of known three-dimensional structure are described. The conditions of the modification have provided suitable yields of the modified complex and allowed characterization of the modified segments of the protein. The potential of tetracycline as a fine modifying reagent was established. In the complex of TetR(D) protein with tetracycline, the antibiotic modifies at least two segments, Ile59-Glu73 and Ala173-Glu183, which form a binding tunnel for the drug according to the X-ray analysis. These data open possibilities for the use of different tetracycline targets for structural studies in solution.

The Tetracycline Repressor-A Paradigm for a Biological Switch

The excessive use of antibiotics has enabled bacteria to develop resistance through a variety of mechanisms. The most common bacteriostatic action of the broad-spectrum antibiotic tetracycline (Tc) is by the inactivation of the bacterial ribosome so that the protein biosynthesis is interrupted and the bacteria die. The most common mechanism of resistance in gram-negative bacteria against Tc is associated with the membrane-intrinsic protein TetA, which exports invaded Tc out of the bacterial cell before it can attack its target, the ribosome. The expression of TetA is tightly regulated by the homodimeric Tet repressor (TetR)(2), which binds specifically with two helix-turn-helix motifs of operator DNA (tetO; K(ass) approximately 10(11) M(-1)) located upstream from the tetA gene on a plasmid or transposon. When Tc diffuses into the cell it chelates Mg(2+) and the complex [MgTc](+) binds to (TetR)(2) to form the induced complex (TetR small middle dot[MgTc](+))(2). This process is associated with conformational changes, which sharply reduce the affinity of (TetR)(2) to tetO, so that expression of TetA can take place, thus conferring resistance to the bacteria cells against Tc. Crystallographic studies show sequence-specific protein-nucleic acid interactions in the (TetR)(2) small middle dottetO complex and how the binding of two [MgTc](+) to (TetR)(2) enforces conformational changes that are stabilized by cooperative binding of two chains of eight water molecules each so that the formed (TetR small middle dot[MgTc](+))(2) is no longer able to recognize and bind to tetO. Since the switching mechanisms of the TetR/[MgTc](+) system is so tight, it has proven very useful in the regulation of eukaryotic gene expression and may also be applicable in gene therapy.

Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system

The tetracycline repressor (TetR) regulates the most abundant resistance mechanism against the antibiotic tetracycline in grain-negative bacteria. The TetR protein and its mutants are commonly used as control elements to regulate gene expression in higher eukaryotes. We present the crystal structure of the TetR homodimer in complex with its palindromic DNA operator at 2.5 A resolution. Comparison to the structure of TetR in complex with the inducer tetracycline-Mg2+ allows the mechanism of induction to be deduced. Inducer binding in the repressor core initiates conformational changes starting with C-terminal unwinding and shifting of the short helix a6 in each monomer. This forces a pendulum-like motion of helix a4, which increases the separation of the attached DNA binding domains by 3 A, abolishing the affinity of TetR for its operator DNA.

Crystallization and preliminary X-ray analyses of catabolite control protein A, free and in complex with its DNA-binding site

The catabolite control protein (CcpA) from Bacillus megaterium is a member of the bacterial repressor protein family GalR/LacI. CcpA with an N-terminal His-tag was used for crystallization. Crystals of free CcpA and of CcpA in complex with the putative operator sequence (catabolite responsive elements, CRE) were obtained by vapour-diffusion techniques at 291 K using the hanging-drop method. CcpA crystals grown in the presence of polyethylene glycol 8000 belong to the hexagonal space group P6(1)22 or P6(5)22, with unit-cell parameters a = 74.4, c = 238.8 A. These crystals diffract X-rays to 2.55 A resolution and contain one monomer of the homodimeric protein per asymmetric unit. Crystals of the CcpA-CRE complex were obtained with ammonium sulfate as precipitant and belong to the tetragonal space group I4(1)22, with unit-cell parameters a = 125, c = 400 A and one complex per asymmetric unit. Although these co-crystals grew to a sufficient size, X-ray diffraction was limited to 8 A resolution.

Structural analysis of an RNase T1 variant with an altered guanine binding segment

The ribonuclease T1 variant 9/5 with a guanine recognition segment, altered from the wild-type amino acid sequence 41-KYNNYE-46 to 41-EFRNWQ-46, has been cocrystallised with the specific inhibitor 2'-GMP. The crystal structure has been refined to a crystallographic R factor of 0.198 at 2.3 A resolution. Despite a size reduction of the binding pocket, pushing the inhibitor outside by 1 A, 2'-GMP is fixed to the primary recognition site due to increased aromatic stacking interactions. The phosphate group of 2'-GMP is located about 4.2 A apart from its position in wild-type ribonuclease T1-2'-GMP complexes, allowing a Ca(2+), coordinating this phosphate group, to enter the binding pocket. The crystallographic data can be aligned with the kinetic characterisation of the variant, showing a reduction of both, guanine affinity and turnover rate. The presence of Ca(2+) was shown to inhibit variant 9/5 and wild-type enzyme to nearly the same extent.

Crystallization and preliminary X-ray diffraction studies of Streptococcus pyogenes plasmid pSM19035-encoded omega transcriptional repressor

The transcriptional repressor, omega protein, from the Streptococcus pyogenes broad-host-range plasmid pSM19035 was crystallized at pH 7. 5 and 8.5 by the vapour-diffusion method using PEG 4000 as precipitant. Two crystal forms were obtained; the first belongs to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2 and the second to the hexagonal space group P6(1) or P6(5). The crystals are most likely to contain one omega protein in the asymmetric unit, with V(m) values of 3.2 and 3.5 A(3) Da(-1), respectively. The crystals diffract X-rays to 2.4 and 2.9 A resolution for the tetragonal and hexagonal systems, -respectively.

Proteolytic cleavage of gram-positive beta recombinase is required for crystallization

Beta recombinase, a DNA resolvase-invertase, catalyzes in the presence of a chromatin-associated protein such as Hbsu, DNA resolution or DNA inversion on supercoiled substrates containing two directly or inversely oriented target (six) sites. Single crystals of the beta recombinase from plasmid pSM19035 were obtained using the vapor diffusion technique with ammonium phosphate as the precipitating agent. The crystals diffracted X-rays to a maximum resolution of 2.5A. Due to proteolytic degradation during the crystallization experiment, the crystals contain only the N-terminal catalytic domain of beta recombinase corresponding to about 60% of the molecular mass of the initially assayed native protein. The proteolytic removal of the C-terminal DNA-binding domain demonstrated that protein modification can be essential to provide material suitable for X-ray analysis.

Crystal structure of the tet repressor in complex with a novel tetracycline, 9-(N,N-dimethylglycylamido)- 6-demethyl-6-deoxy-tetracycline

The tetracycline analog 9-(N, N-dimethylglycylamido)-6-demethyl-6-deoxy-tetracycline (9glyTc) belongs to a new group of tetracyclines called glycylcyclines. They are strong antibiotics showing reduced sensitivity against the major tetracycline resistance mechanisms. We have determined the crystal structure of 9glyTc in complex with Tet repressor class D, TetR(D), at 2.4 A resolution. Sterical hindrance at the entrance of the tetracycline binding tunnel of TetR by the bulky and charged glycyl amido substituent interferes with conformational changes required for the mechanism of induction, and leads to decreased induction efficiency as observed for point mutations of amino acid residues located in the neighbourhood to the glycylamido moiety of bound 9glyTc.

Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus

The N and C termini of peptides presented by major histocompatibility complex (MHC) class I molecules are held within the peptide binding groove by a network of hydrogen bonds to conserved MHC residues. However, the published structure of the human allele HLA-B*3501 complexed with the nef octa-peptide VPLRPMTY, revealed non-standard positioning for both peptide termini. To investigate whether these deviations are indeed related to the length of the nef-peptide, we have determined the structure of HLA-B*3501 presenting a nona-peptide to 2.5 A resolution. A comparison of HLA-B*3501/peptide complexes with structures of other HLA molecules exhibits allele-specific properties of HLA-B*3501, as well as peptide-induced structural changes. Independent of the length of the bound peptide, HLA-B*3501 positions the peptide C terminus significantly closer to the alpha1-helix and nearer to the A pocket than observed for other HLA class I/peptide complexes. This reorientation is accompanied by a shift within the N-terminal part of the alpha2-helix towards the middle of the binding groove. Due to the short distance between the N and C termini, the nona-peptide is compressed and forced to zig-zag vertically within the binding groove. Its conformation rather resembles that of a deca-peptide than of other nona-peptides bound to class I molecules. Superposition of both HLA-B*3501/peptide complexes additionally reveals a significant, peptide-dependent deviation between the N-terminal parts of the alpha1-helices which might be due to different positioning of the peptide N termini. Taken together, these data illustrate the strong interdependence between the HLA class I molecule and the bound peptide.

Tetracycline-chelated Mg2+ ion initiates helix unwinding in Tet repressor induction

The homodimeric tetracycline repressor (TetR) regulates resistance to the antibiotic tetracycline at the transcriptional level. TetR binds in the absence of Tc to palindromic operator sequences utilizing two helix-turn-helix (HTH) motifs. If the tetracycline-Mg2+ complex [MgTc]+ enters two identical binding tunnels buried within the TetR homodimer, a conformational change takes place, and the induced [TetR/[MgTc]+]2 complex releases operator DNA. To demonstrate the contribution of Mg2+ to [MgTc]+ binding and TetR induction, the Mg2+ concentration in the induced TetR homodimer was progressively reduced by addition of EDTA, resulting in two X-ray crystal structures of Mg2+-free and half-occupied TetR(D). Tc remains bound to the [MgTc]+-binding sites, despite the complete or partial absence of Mg2+. Together with inducer-free TetR(D), the structures were refined to between 2.2 and 2.7 A resolution and compared with fully induced TetR(D) in complex with two [MgTc]+. Each inducer binding tunnel has three constituent parts, one hydrophobic and two hydrophilic ones. One of the hydrophilic contact areas binds Tc by hydrogen bonding; the hydrophobic region correctly positions Tc and partially closes the entrance to the binding tunnel; the second hydrophilic region coordinates Mg2+, transduces the induction signal, and completes the process of closing the tunnel entrance. Tc confers binding specificity to TetR while Mg2+ is primarily responsible for induction: After binding to the imidazole Nepsilon of His100, Mg2+ is octahedrally coordinated to the 1,3-ketoenolate group of Tc and to three water molecules. One of these waters forms a hydrogen bond to the hydroxyl group Ogamma of Thr103. The induced 2.5 A movement of Thr103 results in the partial unwinding of helix alpha6, associated with a lateral shift of helices alpha4 and alpha9. They simultaneously close the tunnel entrance and cause the DNA-binding domains to adopt a nonbinding conformation, leading to release of operator DNA and expression of the genes responsible for resistance.

Conformational changes of the Tet repressor induced by tetracycline trapping

The X-ray crystal structure analysis of inducer-free Tet repressor, TetR, at 2.4 A resolution identifies one of two openings of the tunnel-like binding site as the entrance for the inducer tetracycline-Mg2+, [Mg Tc]+. Recognition and binding of the inducer unleashes conformational changes leading to the induced state of TetR. In the first step, the C-terminal turn of alpha-helix 6 unwinds, thereby altering the orientation of alpha-helix 4. This different orientation of alpha-helix 4 is stabilized by a series of hydrogen bonds mediated through a chain of eight water molecules. The alpha-helix 4 connects the DNA-binding domain (alpha-helices 1 to 3) to the rigid TetR core, and thus regulates gene expression through its respective orientations.

Raman spectroscopic analysis of Tet repressor-operator DNA interaction in deuterium oxide

Tet repressor (TetR) plays a central role in the regulation of its own gene and in that of TetA, a resistance protein against the antibiotic tetracycline (Tc). In the absence of Tc, the TetR dimer binds with two alpha-helix-turn-alpha-helix motifs to two successive major grooves of operator DNA. In order to elucidate structural features of the TetR:operator complex, we measured the Raman spectra of the TetR protein, a 18-mer oligonucleotide with sequence corresponding to TetR operator DNA, and the TetR:operator complex in D2O. The spectra confirm and extend previously obtained results in H2O: i) B-DNA conformation is conserved with only small perturbations of the backbone geometry; ii) TetR and operator DNA interact at major groove sites, as evident from intensity changes of thymine and guanine bands; iii) Minor changes of TetR secondary structure are indicated upon operator binding, and iv) Local environments of aromatic amino acids are altered in the complex. These spectroscopic findings are consistent with a molecular model proposed of the basis of genetic and biochemical studies.

Interaction of Tet repressor with operator DNA and with tetracycline studied by infrared and Raman spectroscopy

Tet repressor (TetR) is involved in the most abundant mechanism of tetracycline (Tc) resistance of gram-negative bacteria. Raman spectra were measured for the class D TetR protein, for an oligodeoxyribonucleotide with sequence corresponding to operator site O1, and for the TetR:oligonucleotide complex. TetR forms a complex with [Ni-Tc]+, which does not bind to operator DNA. Raman and infrared measurements indicate nearly identical conformations of TetR with and without [Ni-Tc]+. Differences between the experimental spectrum of the TetR:operator DNA complex and the computed sum of the component spectra provide direct spectroscopic evidence for changes in DNA backbone torsions and base stacking, rearrangement of protein backbone, and specific contacts between TetR residues and DNA bases. Complex formation is connected with intensity decrease at 1376 cm(-1) (participation of thymine methyl groups), intensity increase at 1467 cm(-1) (hydrogen bond formation at guanine N7), decreased intensity ratio I854/I823 (increased hydrophobicity of tyrosine environment), increased intensity at 1363 cm(-1) (increased hydrophobicity of tryptophan ring environment), differences in the range 670-833 cm(-1) (changes in B-DNA backbone torsions and base stacking), and decreased intensity of the amide I band (structural rearrangement of TetR backbone consistent with a reduction of the distance between the two binding helices).

Crystallization and preliminary X-ray analysis of the Tet-repressor/operator complex

Three crystal forms of the repressor protein TetR class D in complex with the palindromic 17 bp operator sequence containing T overhangs on both sides were obtained by hanging-drop vapor-diffusion methods using PEG 4000 and PEG monomethylether 5000 as precipitants. Although the crystallization conditions were very similar, up to three different crystal forms were observed in the same drop. The space groups are monoclinic C2, P21 and hexagonal P6122. The asymmetric units of the latter two crystal forms contain one repressor-operator complex. The crystal structures of these forms were solved by molecular replacement using the Tet-repressor molecule of the complex with tetracycline as a search model.