Use of a heterodimeric coiled-coil system for biosensor application and affinity purification

The two-stranded alpha-helical coiled-coil is now recognized as one of nature's favorite ways of creating a dimerization motif. Based on the knowledge of protein folding studies and de novo design model systems, a novel heterodimeric coiled-coil protein was synthesized. The heterodimeric E/K coiled-coil was constructed with two distinct peptides (E and K) that will spontaneously associate into a full helical coiled-coil structure in solution. Equilibrium CD, NMR and real time biosensor kinetics experiments showed that the E/K coiled-coil is both structurally (deltaG(unfold)=11.3 kcal/mol) and kinetically (Kd approximately 1 nM) stable in solution at neutral pH. The engineered coiled-coil had been applied as a dimerization and capture domain for biosensor based applications and used in an expression/detection/affinity chromatography system. Specific test examples demonstrated the usefulness of the E/K heterodimeric system in these applications. The universality of coiled-coil as a dimerization motif in nature and our ability to design and synthesize these proteins suggest a wide variety of applications.

Binding of an oligopeptide to a specific plane of ice

The alpha-helical antifreeze protein (AFP) from winter flounder inhibits ice growth by binding to a specific set of pyramidal surface planes that are not otherwise macroscopically expressed. The 37-residue AFP contains three 11-amino acid repeats that make a stereo-specific fit to the ice lattice along the <01-12> direction of the (20-21) and equivalent binding planes. When the AFP was shortened to delete two of the three 11-amino acid ice-binding repeats, the resulting 15-residue peptide and its variants were less helical and showed no antifreeze activity. However, when the helicity of the peptide was reinforced by an internal lactam bridge between Glu-7 and Lys-11, the minimized AFP was able to stably express the pyramidal plane (20-21) on the surface of growing ice crystals. This dynamic shaping of the ice surface by a single ice-binding repeat provides evidence that AFP adsorption to the ice lattice is not an "all-or-nothing" interaction. Instead, a partial interaction can help develop the binding site on ice to which the remainder of the AFP (or other AFP molecules) can orient and bind.

Effect of mobile phase on the oligomerization state of alpha-helical coiled-coil peptides during high-performance size-exclusion chromatography

Important structural motifs involving amphipathic helices include two-stranded and multiple-stranded coiled-coils. High-performance size-exclusion chromatography (HPSEC) is a useful tool to examine both the oligomerization state of coiled-coils as well as the stability of such motifs, due to the facile manipulation of the mobile phase and the lack of interaction of the peptide solutes with the stationary phase. In the present study, HPSEC was applied to two series of de novo designed model amphipathic alpha-helical peptides with the sequences (1) Ac-(E-A-L-K-A-E-I)n-E-A-C-K-A-amide, where n = 1 or 3, Ac-E-I-(E-A-L-K-A-E-I)4-E-A-C-K-A-amide and (2) Ac-(K-L-E-A-L-E-A)n-amide, where n = 1, 2 or 4. Observation of the retention behaviour of Series 1 under both denaturing and non-denaturing conditions at pH 7.0 offered insights into the effect of polypeptide chain length and disulphide bridge formation on the stability of alpha-helical coiled-coils. In contrast, the Series 2 peptides showed promise as peptide standards to monitor the effect of environment on the multi-strandedness of coiled-coils, since the 28-residue peptide of this series was eluted as a monomer, dimer or trimer depending on mobile phase conditions.

A diminished role for hydrogen bonds in antifreeze protein binding to ice

The most abundant isoform (HPLC-6) of type I antifreeze protein (AFP1) in winter flounder is a 37-amino-acid-long, alanine-rich, alpha-helical peptide, containing four Thr spaced 11 amino acids apart. It is generally assumed that HPLC-6 binds ice through a hydrogen-bonding match between the Thr and neighboring Asx residues to oxygens atoms on the {2021} plane of the ice lattice. The result is a lowering of the nonequilibrium freezing point below the melting point (thermal hysteresis). HPLC-6, and two variants in which the central two Thr were replaced with either Ser or Val, were synthesized. The Ser variant was virtually inactive, while only a minor loss of activity was observed in the Val variant. CD, ultracentrifugation, and NMR studies indicated no significant structural changes or aggregation of the variants compared to HPLC-6. These results call into question the role of hydrogen bonds and suggest a much more significant role for entropic effects and van der Waals interactions in binding AFP to ice.

RARE imaging of PCr in human forearm muscles

Rapid acquisition with relaxation enhancement (RARE) sequences have been used to map the 31P phosphocreatine (PCr) signal in human forearms at 4.7 T. Signal-to-noise levels of approximately 10 were achieved from the major muscle groups in 5.5-minute scan times with a spatial resolution of 4 x 2 x 2 cm3. Exercise caused demonstrable reductions in PCr signal from activated muscles, which correlated with affected muscle groups in T2-weighted proton images. RARE imaging of the PCr signal at 4.7 T is feasible and, with technically achievable improvements in signal-to-noise ratio, should prove useful in studying energy metabolism in muscle and other organs.

Multiecho approaches to spectroscopic imaging of the brain

Spectroscopic imaging (SI) with nuclear magnetic resonance (NMR) is one of the most powerful tools available for studying brain chemistry in vivo. Both proton (1H) and phosphorus (31P) NMR offer valuable biochemical information that can in principle be mapped throughout the entire brain, thereby enhancing our understanding of brain function. With the exception of protons from tissue water and the triglycerides of adipose tissue, however, nuclei contributing to the NMR signals of living tissue are in relatively small (millimolar) concentrations. The low concentration of metabolite nuclei reduces the overall sensitivity of conventional SI techniques, making high-quality metabolite mapping a lengthy procedure. This problem has led to the development and testing of nonconventional methods for reducing SI scan times, including techniques based on the collection of multiple spin-echoes. The extent to which multiecho methods can be used to decrease SI scan times and maintain high-quality metabolite mapping depends on several factors. These include the spectral transverse relaxation times, the spectral resolution required, and J-coupling interactions. We have discussed these various technical aspects of multiecho SI methods as applied to 1H and 31P spectroscopic imaging of the living brain.

[Clonal analysis of blood cells using X-linked HUMARA gene polymorphism]

OBJECTIVE

To explore the method for clonal analysis of blood cells.

METHODS

Thirty female AML patients and 20 normal female subjects were analysed by the analysis of X-linked HUMARA gene polymorphism and methylation pattern.

RESULTS

The heterozygote rate of HUMARA gene in Chinese women was 88% and the gene had a stable methylation pattern. Out of 20 control females, 17 were heterozygotes and among them 15 were polyclonal, 2 (11.8%) showed skewed X-inactivation. All heterozygote AML were clonal hematopoiesis.

CONCLUSION

HUMARA gene polymorphism is a good marker for clonality analysis of blood cells.

Multibolus stimulated echo imaging of coronary artery flow

One limitation of traditional bolus tagging techniques for MR angiography is the small amount of blood labeled by one tagging, resulting in a limited filling of the downstream vessels. We describe a multiple bolus technique using stimulated echoes (STE) for imaging coronary flow. A series of radiofrequency (RF) pairs are given with each pair selective at the region of tagging, thus tagging consecutive volumes of blood, and a final nonselective pulse is given to "read out" all of the tagged spins. In this way, multiple boluses of tagged blood are imaged at one time.

Multi-echo 31P spectroscopic imaging of ATP: a scan time reduction strategy

Spectroscopic imaging of 31P metabolites and adenosine triphosphate (ATP) in particular with multiple spin echoes may prove useful for reducing data acquisition times. The usual T2 decay processes that degrade multi-echo spectroscopic imaging methods, however, are further compounded by J-coupling modulations in the case of ATP. We determine how these modulations affect multi-echo spectroscopic imaging k-space data and produce systematic spatial misregistrations of the ATP resonances. The specific J-coupling modulations of ATP are determined to identify echo-spacing effects in multi-echo spectroscopic imaging of ATP and to determine appropriate post-processing correction schemes to address the spatial misregistration problem. An in vivo demonstration of the technique that offers a threefold reduction in scan time compared to conventional SI methods is provided and compared with the conventional SI approach.

[A clinical analysis of 153 uterine sarcomas]

OBJECTIVE

To evaluate the prognostic factors and treatment methods of 153 uterine sarcomas.

METHODS

153 cases of the uterine sarcoma were eligible for this retrospective study. Of the 153 cases, 48 were leiomyosarcomas, 47 mixed mesodermal sarcomas, 37 endometrial stromal sarcomas, 8 carcinosarcomas, 4 sarcoma botryoides, 1 fibrosarcoma, and 8 malignant lymphomas. 81 cases were in stage I, 11 stage II, 33 stage III and 11 stage IV. 38 cases were treated by surgery alone, 24 by surgery combined with radiation therapy, 50 by surgery plus chemotherapy, 23 by surgery plus radiation therapy and chemotherapy, 4 by radiation therapy alone, 3 by chemotherapy alone, and 11 by radiation therapy plus chemotherapy.

RESULTS

The overall 5-year survival rate was 49.0%, and that of leiomyosarcomas, mixed mesodermal sarcomas and endometrial stromal sarcomas was 46.9%, 34.1% and 69.3% respectively (P < 0.01). The 5-year survival rate of lesions limited to the uterus (stage I + II), and that of pelvic cavity invasion (stage III) and distant metastases was 59.6%, 25.6% and 10.0% respectively (P < 0.01. When the uterus was smaller than a 3 months pregnant uterus, the 5-year survival rate was 49.9%. When the uterus size larger than a 3 months pregnant uterus, the survival rate was 18.8% (P < 0.05). Premenopausals surviving 5-year accounted for 56.3% and post-menopausal 28.9% (P < 0.01).

CONCLUSIONS

The prognosis of uterine sarcoma is significantly associated with histologic type, clinical and surgico-pathological stage, uterine size and pre- or post-menopausal status. Radiation or chemotherapy alone is palliative. Postsurgical adjuvant radiotherapy significantly decreased vaginal and pelvic recurrences rates. A combination of surgery, radiotherapy and chemotherapy can reduce pelvic recurrence as well as enhance survivals.

Two novel mutations in phenylalanine hydroxylase gene and in vitro expression analysis on mutation Arg252Gln

We report novel mutations in exon 7 of human phenylalanine hydroxylase (PAH) gene of phenylketonuria (PKU) in southern Chinese, analysed by using PCR-DGGE (denaturing gradient gel electrophoresis), solid phase DNA sequencing and in vitro expression. One of the 2 novel mutations, IVS6nt-1, is an intron-exon junctional mutation which results a splicing defect in mRNA. Arg252Gln is another novel mutation with residual PAH activity only 24% compared to wild type in in vitro mutagenesis and expression in Cos-1 cell. Other 3 known mutations and polymorphism including Arg241Cys, Arg243Gln and Val245Val (GTG to GTA) together with these novel mutations composed the mutational profile of exon 7 in the PAH gene of PKUs in this populations.

[Preliminary study on oncogene MDM2 in acute leukemias]

OBJECTIVE

To explore the causes of MDM2 gene overexpression.

METHODS

The amplification and overexpression of MDM2 gene in 41 acute leukemia patients and two leukemic cell lines (K051 and HL60) were studied by using Southern blot, dot hybridyzation and RT-PCR techniques.

RESULTS

Overexpression of MDM2 gene was found in 51.2% (21/41) of the patients and HL60 cell line, but no amplification of the gene was found in all the patients and the two cell lines.

CONCLUSION

The level of MDM2 gene expression was related to the prognoses of the patients but not to FAB subtypes of acute leukemias.

NMR characterization of side chain flexibility and backbone structure in the type I antifreeze protein at near freezing temperatures

The flexibility of the polar side chains in the alpha-helical Type I antifreeze protein (AFP) near the solution freezing temperature was investigated by two-dimensional nuclear magnetic resonance spectroscopy. These experiments were conducted to define the rotameric conformations of the proposed ice-binding groups, threonines and asparagines, in order to probe the molecular mechanism for ice binding. On the basis of the 3J alpha beta 2 NMR coupling constant values of 7.1, 8.5, 8.5, and 6.8 Hz for residues T2, T13, T24, and T35, respectively, it can be calculated that the regularly spaced ice-binding threonines sample many possible rotameric states prior to ice binding. The lack of a dominant side chain rotamer is further corroborated by nuclear Overhauser distance measurements for T13 and T24. N16 and N27, both with 3J alpha beta 2 and 3J alpha beta 3 coupling constants of 8.4 and 4.5 Hz, respectively, show a slight preference for the side chain conformation with a chi 1 of -60 degrees. These data suggest that prior to ice binding the threonine and asparagine side chains are free to rotate and that a unique preformed ice-binding structure in solution is not apparent. These observations do not support the rigid side chain model proposed recently by an X-ray study [Sicheri, F., & Yang, D. S. C. (1995) Nature 375, 427-431].

Structural basis for the binding of a globular antifreeze protein to ice

Antifreeze proteins (AFPs) have the unique ability to adsorb to ice and inhibit its growth. Many organisms ranging from fish to bacteria use AFPs to retard freezing or lessen the damage incurred upon freezing and thawing. The ice-binding mechanism of the long linear alpha-helical type I AFPs has been attributed to their regularly spaced polar residues matching the ice lattice along a pyramidal plane. In contrast, it is not known how globular antifreeze proteins such as type III AFP that lack repeating ice-binding residues bind to ice. Here we report the 1.25 A crystal structure of recombinant type III AFP (QAE isoform) from eel pout (Macrozoarces americanus), which reveals a remarkably flat amphipathic ice-binding site where five hydrogen-bonding atoms match two ranks of oxygens on the [1010] ice prism plane in the <0001> direction, giving high ice-binding affinity and specificity. This binding site, substantiated by the structures and properties of several ice-binding site mutants, suggests that the AFP occupies a niche in the ice surface in which it covers the basal plane while binding to the prism face.

Effect of type III antifreeze protein dilution and mutation on the growth inhibition of ice

Mutation of residues at the ice-binding site of type III antifreeze protein (AFP) not only reduced antifreeze activity as indicated by the failure to halt ice crystal growth, but also altered ice crystal morphology to produce elongated hexagonal bipyramids. In general, the c axis to a axis ratio of the ice crystal increased from approximately 2 to over 10 with the severity of the mutation. It also increased during ice crystal growth upon serial dilution of the wild-type AFP. This is in marked contrast to the behavior of the alpha-helical type I AFPs, where neither dilution nor mutation of ice-binding residues increases the c:a axial ratio of the ice crystal above the standard 3.3. We suggest that the ice crystal morphology produced by type III AFP and its mutants can be accounted for by the protein binding to the prism faces of ice and operating by step growth inhibition. In this model a decrease in the affinity of the AFP for ice leads to filling in of individual steps at the prism surfaces, causing the ice crystals to grow with a longer c:a axial ratio.

Kinetic study on the formation of a de novo designed heterodimeric coiled-coil: use of surface plasmon resonance to monitor the association and dissociation of polypeptide chains

The surface plasmon resonance (SPR) technique was used to study the formation kinetics of a de novo designed coiled-coil (E/K coil). The E/K coil is made up of two distinct peptides (E and K) each with five heptad (g-a-b-c-d-e-f) repeats. The E peptide's heptad sequence is E-V-S-A-L-E-K, and the K peptide's heptad sequence is K-V-S-A-L-K-E. A linker C-nL-G-G-G (nL = norleucine) is present at the C-terminus of the E peptide and at the N-terminus of the K peptide for the SPR studies. Heterodimer formation involves both electrostatic and hydrophobic interactions at the dimer interface. Under conditions that favor the heterodimer formation, the CD signal ([theta]222) varied as a function of peptide concentration. The estimated dissociation constant (Kd) was 2.45 +/- 0.71 nM. Denaturation studies with guanidine-HCI (GdnHC11/2 = 3.9 M) suggested a value of 3.53 +/- 0.48 nM. For the SPR investigation, the peptides were biotinylated and linked to streptavidin in order to increase their effective molecular weight and consequently enhance the signal intensity. Biotinylation in itself did not impede coiled-coil formation based on CD measurements. The biosensor study revealed a slow dissociation rate constant for the heterodimer (kd approximately 2 x 10(-4) s-1) and a moderately fast association rate constant [ka approximately (4.27-4.53) x 10(5) M-1 s-1). This gives a calculated Kd of 0.47-0.50 nM, which agrees reasonably well with the equilibrium CD studies. Therefore, based on the SPR data, the preference for heterodimer formation is due to a combination of moderately fast association and slow dissociation rates.

Effects of antifreeze proteins on red blood cell survival during cryopreservation

Antifreeze protein (AFP) types, I, II and III were tested for their ability to protect red blood cells from lysis during warming, after cryopreservation in hydroxyethyl starch. All three types reduced hemolysis to 25% of control values at similar micromolar concentrations but enhanced lysis as the AFP concentration approached millimolar levels. Site-directed mutants of type III AFP with different thermal hysteresis activities were tested for their ability to protect the cryopreserved cells from lysis. Their relative efficacy in protecting the cells correlated closely with their thermal hysteresis activity. Cryomicroscopy indicated that the protection of red cells by type III AFP and the mutant forms was due to inhibition of ice recrystallization.

A natural variant of type I antifreeze protein with four ice-binding repeats is a particularly potent antifreeze

A 4.3-kDa variant of Type I antifreeze protein (AFP9) was purified from winter flounder serum by size exclusion chromatography and reversed-phase HPLC. By the criteria of mass, amino acid composition, and N-terminal sequences of tryptic peptides, this variant is the posttranslationally modified product of the previously characterized AFP gene 21a. It has 52 amino acids and contains four 11-amino acid repeats, one more than the major serum AFP components. The larger protein is completely alpha-helical at 0 degree C, with a melting temperature of 18 degrees C. It is considerably more active as an antifreeze than the three-repeat winter flounder AFP and the four-repeat yellowtail flounder AFP, both on a molar and a mg/mL basis. Several structural features of the four-repeat winter flounder AFP, including its larger size, additional ice-binding residues, and differences in ice-binding motifs might contribute to its greater activity. Its abundance in flounder serum, together with its potency as an antifreeze, suggest that AFP9 makes a significant contribution to the overall freezing point depression of the host.

[Late bladder complications following radiotherapy of carcinoma of the uterine cervix]

OBJECTIVE

To analyse the causes, clinical features, treatment and prevention of late bladder complications following radiotherapy of carcinoma of the uterine cervix.

METHOD

This clinical retrospective study included 378 cases of irradiation cystitis following radiotherapy for carcinoma of the uterine cervix from February, 1958 to October, 1987.

RESULTS

The incidence of irradiation cystitis was 3.2% and was not related to age, FIGO staging and the methods of intracavitary irradiation (conventional or afterloading). It was related to the external appearance of the local lesion; 66.5% of the tumors of patients with late bladder complications was of the exophytic type prior to radiotherapy. 51.1% of the patients developed late bladder complications in a period of 2-5 years after radiotherapy; 16.7% in 5-10 years and only 3.4% within the first years. The patients with irradiation cystitis had received a 10% higher dosage than that routine delivered, as found either in intracavitary irradiation of 39.4% of patients or in external irradiation of 31.6% of patients. Based on the clinical features and cystoscopic findings, late bladder complications can be divided into three types: (1) sudden and temporary hematuria (35.7%); (2) persistent hematuria (63.2%); and (3) vesico-vaginal fistula (1.1%). The 5-year survival rate of patients with irradiation cystitis was 90.4% which was higher than the survival rates of all patients treated by conventional intracavitary irradiation (65.7%) and all patients treated by afterloading intracavitary irradiation (70.4%). 3.7% of patients died of late bladder complications.

CONCLUSIONS

To decrease the occurrence of late bladder complications and to obtain long term survival: (1) Dosage to the bladder should be adequate, and over dose to the bladder should by all means be avoided; (2) Patients are to be taught to observe indicated personal care during radiotherapy as well as in the follow-up period; (3) Early institution of proper conservative treatment of cystitis is beneficial.

[Expression of MDM2 gene in acute leukemia]

In order to study expression of MDM2 gene, antagonist of tumor suppressor gene p53 in acute leukemia, forty acute leukemia patients were tested using RT-PCT to evaluate expression level of MDM2 gene. Over-expression of MDM2 gene was found in 52.5% patients (21/40). No significant relations were found between the level of MDM2 gene expression and FAB subtypes of acute leukemia. It is suggested that the over-expression of MDM2 gene may play a role in acute leukemia.

Mixing antifreeze protein types changes ice crystal morphology without affecting antifreeze activity

All three fish antifreeze protein types (I, II and III) inhibit the growth of ice to form hexagonal bipyramidal ice crystals of characteristic morphology. Mixtures of these different antifreezes produced ice crystals of hybrid shapes and dimensions, consistent with the different antifreeze types binding to the same ice surfaces. The activity of the mixtures was independent of the proportions of the iso-active antifreeze protein stocks present, indicating that the different antifreezes neither attenuated nor potentiated each other's activity. We suggest that antifreeze protein molecules are independently active and do not require protein-protein interactions for ice-binding.

Structure-function relationship in the globular type III antifreeze protein: identification of a cluster of surface residues required for binding to ice

Antifreeze proteins (AFPs) depress the freezing point of aqueous solutions by binding to and inhibiting the growth of ice. Whereas the ice-binding surface of some fish AFPs is suggested by their linear, repetitive, hydrogen bonding motifs, the 66-amino-acid-long Type III AFP has a compact, globular fold without any obvious periodicity. In the structure, 9 beta-strands are paired to form 2 triple-stranded antiparallel sheets and 1 double-stranded antiparallel sheet, with the 2 triple sheets arranged as an orthogonal beta-sandwich (Sönnichsen FD, Sykes BD, Chao H, Davies PL, 1993, Science 259:1154-1157). Based on its structure and an alignment of Type III AFP isoform sequences, a cluster of conserved, polar, surface-accessible amino acids (N14, T18, Q44, and N46) was noted on and around the triple-stranded sheet near the C-terminus. At 3 of these sites, mutations that switched amide and hydroxyl groups caused a large decrease in antifreeze activity, but amide to carboxylic acid changes produced AFPs that were fully active at pH 3 and pH 6. This is consistent with the observation that Type III AFP is optimally active from pH 2 to pH 11. At a concentration of 1 mg/mL, Q44T, N14S, and T18N had 50%, 25%, and 10% of the activity of wild-type antifreeze, respectively. The effects of the mutations were cumulative, such that the double mutant N14S/Q44T had 10% of the wild-type activity and the triple mutant N14S/T18N/Q44T had no activity. All mutants with reduced activity were shown to be correctly folded by NMR spectroscopy. Moreover, a complete characterization of the triple mutant by 2-dimensional NMR spectroscopy indicated that the individual and combined mutations did not significantly alter the structure of these proteins. These results suggest that the C-terminal beta-sheet of Type III AFP is primarily responsible for antifreeze activity, and they identify N14, T18, and Q44 as key residues for the AFP-ice interaction.

Use of proline mutants to help solve the NMR solution structure of type III antifreeze protein

To help understand the structure/function relationships in antifreeze proteins (AFP), and to define the motifs required for ice binding, a Type III AFP suitable for two-dimensional (2D) NMR studies was produced in Escherichia coli. A synthetic gene for one of the Type III AFP isoforms was assembled in a T7 polymerase-directed expression vector. The 67-amino acid-long gene product differed from the natural AFP by inclusion of an N-terminal methionine but was indistinguishable in activity. The NMR spectra of this AFP were complicated by cis-trans proline isomerization from the C-terminal sequence YPPA. Substitution of this sequence by YAA eliminated isomer signals without altering the activity or structure of the mutant AFP. This variant (rQAE m1.1) was selected for sequential assignment and the secondary structure determination using 2D 1H NMR spectroscopy. Nine beta-strands are paired to form two triple-stranded antiparallel sheets and one double-stranded antiparallel sheet. Two further proline replacements, P29A and P33A, were made to delineate the role of conserved prolines in Type III AFP. These mutants were valuable in clarifying ambiguous NMR spectral assignments amongst the remaining six prolines of rQAE m1.1. In contrast to the replacement of the C-terminal prolyl residues, the exchange of P29 and P33 caused some structural changes and significantly decreased protein solubility and antifreeze activity.

The nonhelical structure of antifreeze protein type III

Antifreeze proteins (AFPs) are present in the blood of some marine fishes and inhibit the growth of ice crystals at subzero temperatures by adsorption to the ice lattice. The solution structure of a Type III AFP was determined by two-dimensional nuclear magnetic resonance spectroscopy. These measurements indicate that this 66-residue protein has an unusual fold in which eight beta strands form two sheets of three antiparallel strands and one sheet of two antiparallel strands, and the triple-stranded sheets are packed orthogonally into a beta sandwich. This structure is completely different from the amphipathic, helical structure observed for Type I AFPs.