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1.
Sci Robot ; 9(88): eadh8332, 2024 Mar 13.
Article in English | MEDLINE | ID: mdl-38478590

ABSTRACT

Ice worlds are at the forefront of astrobiological interest because of the evidence of subsurface oceans. Enceladus in particular is unique among the icy moons because there are known vent systems that are likely connected to a subsurface ocean, through which the ocean water is ejected to space. An existing study has shown that sending small robots into the vents and directly sampling the ocean water is likely possible. To enable such a mission, NASA's Jet Propulsion Laboratory is developing a snake-like robot called Exobiology Extant Life Surveyor (EELS) that can navigate Enceladus' extreme surface and descend an erupting vent to capture unaltered liquid samples and potentially reach the ocean. However, navigating to and through Enceladus' environment is challenging: Because of the limitations of existing orbital reconnaissance, there is substantial uncertainty with respect to its geometry and the physical properties of the surface/vents; communication is limited, which requires highly autonomous robots to execute the mission with limited human supervision. Here, we provide an overview of the EELS project and its development effort to create a risk-aware autonomous robot to navigate these extreme ice terrains/environments. We describe the robot's architecture and the technical challenges to navigate and sense the icy environment safely and effectively. We focus on the challenges related to surface mobility, task and motion planning under uncertainty, and risk quantification. We provide initial results on mobility and risk-aware task and motion planning from field tests and simulated scenarios.

2.
J Dent Res ; 97(10): 1152-1159, 2018 09.
Article in English | MEDLINE | ID: mdl-29879365

ABSTRACT

Transplantation of bone marrow mesenchymal stem cells (BMDCs) into a denervated side of the spinal cord was reported to be a useful option for axonal regeneration. The innervation of teeth is essential for their function and protection but does not occur spontaneously after injury. Cultured reassociations between dissociated embryonic dental mesenchymal and epithelial cells and implantation lead to a vascularized tooth organ regeneration. However, when reassociations were coimplanted with a trigeminal ganglion (TG), innervation did not occur. On the other hand, reassociations between mixed embryonic dental mesenchymal cells and bone marrow-derived cells isolated from green fluorescent protein (GFP) transgenic mice (BMDCs-GFP) (50/50) with an intact and competent dental epithelium (ED14) were innervated. In the present study, we verified the stemness of isolated BMDCs, confirmed their potential role in the innervation of bioengineered teeth, and analyzed the mechanisms by which this innervation can occur. For that purpose, reassociations between mixed embryonic dental mesenchymal cells and BMDCs-GFP with an intact and competent dental epithelium were cultured and coimplanted subcutaneously with a TG for 2 wk in ICR mice. Axons entered the dental pulp and reached the odontoblast layer. BMDCs-GFP were detected at the base of the tooth, with some being present in the pulp associated with the axons. Thus, while having a very limited contribution in tooth formation, they promoted the innervation of the bioengineered teeth. Using quantitative reverse transcription polymerase chain reaction and immunostainings, BMDCs were shown to promote innervation by 2 mechanisms: 1) via immunomodulation by reducing the number of T lymphocytes (CD3+, CD25+) in the implants and 2) by expressing neurotrophic factors such as NGF, BDNF, and NT3 for axonal growth. This strategy using autologous mesenchymal cells coming from bone marrow could be used to innervate bioengineered teeth without treatment with an immunosuppressor such as cyclosporine A (CsA), thus avoiding multiple side effects.


Subject(s)
Mesenchymal Stem Cell Transplantation/methods , Tissue Engineering/methods , Tooth/innervation , Animals , Green Fluorescent Proteins , Mesenchymal Stem Cells/physiology , Mice , Mice, Inbred ICR , Mice, Transgenic , Odontogenesis , Tooth/growth & development
3.
Rev Neurol (Paris) ; 173(4): 194-200, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28392062

ABSTRACT

Following a review of the available assessment scales and current practices of evaluation of instrumental activities of daily living (IADL) in French memory centres by GREFON (Groupe de réflexion sur l'évaluation fonctionnelle; Working Group on Functional Assessment), the main aim of this position paper was to provide good clinical practice (GCP) guidelines for the assessment of IADL. Another aim was to highlight the need for innovative tools adapted to the present and future evolution of such activities in real life, including the use of new technologies, the need for earlier detection of IADL impairment during the diagnostic process of mild neurocognitive disorders, and greater sensitivity to IADL changes during follow-up to allow adaptation of clinical management and evaluation of the impact of therapeutic interventions.


Subject(s)
Activities of Daily Living/psychology , Memory Disorders/psychology , Psychometrics , Adult , Aged , Aged, 80 and over , Cognitive Dysfunction/psychology , Cognitive Dysfunction/therapy , Female , France , Guidelines as Topic , Humans , Male , Memory Disorders/therapy , Middle Aged , Neuropsychological Tests , Surveys and Questionnaires
4.
Acta Crystallogr D Biol Crystallogr ; 57(Pt 11): 1677-9, 2001 Nov.
Article in English | MEDLINE | ID: mdl-11679742

ABSTRACT

Numerous precursors of antibacterial peptides with unrelated sequences share a similar prosequence which belongs to the cathelicidin family of proteins. The three-dimensional structure of this cathelicidin motif, which contains two disulfide bonds, has not yet been reported. The cathelicidin motif (ProS) of the protegrin-3 precursor was overexpressed in Escherichia coli as a His-tagged protein. The His(6) tag was removed by thrombin cleavage. ProS was purified to homogeneity and single crystals were obtained by the hanging-drop vapour-diffusion method at pH 3-4. Preliminary X-ray diffraction analysis indicated that these crystals belong to the hexagonal space group P6(1)22 or P6(5)22, with unit-cell parameters a = b = 51.42, c = 134.25 A. These crystals diffracted beyond 2.75 A (1.9 A at ESRF) and contain one molecule per asymmetric unit.


Subject(s)
Proteins/chemistry , Amino Acid Motifs , Antimicrobial Cationic Peptides , Blood Proteins/chemistry , Crystallization , Crystallography, X-Ray , Protein Conformation , Protein Precursors/chemistry , Recombinant Proteins/chemistry
5.
J Immunol ; 167(6): 3139-45, 2001 Sep 15.
Article in English | MEDLINE | ID: mdl-11544299

ABSTRACT

Here we describe the production of a rabbit polyclonal Ab (RAS1) raised against the stalk of murine CD23. RAS1 inhibits release of CD23 from the surface of both M12 and B cells resulting in an increase of CD23 on the cell surface. Despite this increase, these cells are unable to bind IgE as determined by FACS. CD23 has previously been shown to bind IgE with both a high (4-10 x 10(7) M(-1)) and low (4-10 x 10(6) M(-1)) affinity. Closer examination by direct binding of (125)I-IgE revealed that RAS1 blocks high affinity binding while having no effect on low affinity binding. These data support the model proposing that oligomers of CD23 mediate high affinity IgE binding. These experiments suggest that RAS1 binding to cell surface CD23 results in a shift from oligomers to monomers, which, according to the model, only bind IgE with low affinity. These experiments also suggest that high affinity binding of IgE is required for IgE regulation by CD23 and is demonstrated by the fact that treatment of Ag/Alum-immunized mice treated with RAS1 results in a significant increase in IgE production similar to the levels seen in CD23-deficient mice. These mice also had significantly decreased levels of serum soluble CD23 and Ag-specific IgG1. RAS1 had no effect on IgE or Ag-specific IgG1 production in CD23-deficient mice.


Subject(s)
Immunoglobulin E/biosynthesis , Receptors, IgE/physiology , Animals , Antibodies/immunology , Biopolymers , Epitopes/immunology , Flow Cytometry , Gene Expression Regulation/physiology , Immunoglobulin E/genetics , Interleukin-4/pharmacology , Interleukin-5/pharmacology , Lymphoma, B-Cell/pathology , Macromolecular Substances , Mice , Mice, Inbred BALB C , Protein Binding , Protein Conformation , Protein Structure, Tertiary , Rabbits , Receptors, IgE/chemistry , Recombinant Proteins/pharmacology , Tumor Cells, Cultured
6.
Proteins ; 45(2): 117-28, 2001 Nov 01.
Article in English | MEDLINE | ID: mdl-11562941

ABSTRACT

Among the EF-hand Ca(2+)-binding proteins, parvalbumin (PV) and calbindin D9k (CaB) have the function of Ca(2+) buffers. They evolved from an ancestor protein through two phylogenetic pathways, keeping one pair of EF-hands. They differ by the extra helix-loop-helix (AB domain) found in PV and by the linker between the binding sites. To investigate whether the deletion of AB in PV restores a CaB-like structure, we prepared and solved the structure of the truncated rat PV (PVratDelta37) by X-ray and NMR. PVratDelta37 keeps the PV fold, but is more compact, having a well-structured linker, which differs remarkably from CaB. PvratDelta37 has no stable apo-form, has lower affinity for Ca(2+) than full-length PV, and does not bind Mg(2+), in contrast to CaB. Structural differences of the hydrophobic core are partially responsible for lowering the calcium-binding affinity of the truncated protein. It can be concluded that the AB domain, like the linker of CaB, plays a role in structural stabilization. The AB domain of PV protects the hydrophobic core, and is required to maintain high affinity for divalent cation binding. Therefore, the AB domain possibly modulates PV buffer function.


Subject(s)
Calcium-Binding Proteins/chemistry , EF Hand Motifs/physiology , Evolution, Molecular , Parvalbumins/chemistry , Amino Acid Sequence , Animals , Calcium/chemistry , Calcium/metabolism , Calcium-Binding Proteins/physiology , Cations/metabolism , Crystallization , Crystallography, X-Ray , Gene Deletion , Models, Molecular , Molecular Sequence Data , Parvalbumins/genetics , Parvalbumins/physiology , Protein Conformation , Protein Structure, Tertiary , Rats , Recombinant Proteins/chemistry , Sequence Homology, Amino Acid
7.
Schweiz Med Wochenschr ; 130(40): 1407-12, 2000 Oct 07.
Article in German | MEDLINE | ID: mdl-11059032

ABSTRACT

Radiotherapy of breast cancer, cervical cancer, testicular tumours and lymphoma is one of the most effective therapy options. Damage to the nervous system, in particular the brachial and lumbar plexus, is rare and typically leads to development of progressive sensory disturbances and motor weakness after years-long latency. We present two cases exemplifying the diagnostic problems in differentiating between radiation-induced injury and recurrence of the primary tumour. A clinical course with sensorimotor symptoms and signs progressing over months, electomyographic recording of myokymic discharges, and absence of a space-occupying mass suggest late-onset radiation-induced plexopathy. The literature on pathogenesis and incidence of radiation-induced plexopathy is reviewed.


Subject(s)
Autonomic Pathways/physiopathology , Autonomic Pathways/radiation effects , Breast Neoplasms/radiotherapy , Radiation Injuries/diagnosis , Radiotherapy/adverse effects , Uterine Cervical Neoplasms/radiotherapy , Aged , Breast Neoplasms/surgery , Diagnosis, Differential , Female , Humans , Middle Aged , Radiation Injuries/etiology , Recurrence , Uterine Cervical Neoplasms/pathology
9.
Am Heart J ; 137(5): 958-66, 1999 May.
Article in English | MEDLINE | ID: mdl-10220647

ABSTRACT

BACKGROUND: The asymmetry and complex shape of the right ventricle have made it difficult to determine right ventricular (RV) volume with 2-dimensional echocardiography. Three-dimensional cardiac imaging improves visualization of cardiac anatomy but is also complex and time consuming. A newly developed volumetric scanning system holds promise of obviating past limitations. METHODS: Real-time, transthoracic 3-dimensional echocardiographic images of the right ventricle were obtained with a high-speed volumetric ultrasound system that uses a 16:1 parallel processing schema from a 2.5 MHz matrix phased-array scanner to interrogate an entire pyramidal volume in real time. The instrumentation was used to measure RV volume in 8 excised canine hearts; dynamic real-time 3-dimensional images were also obtained from 14 normal subjects. RESULTS: Three-dimensional images were obtained in vitro and in vivo during intravenous hand-agitated saline injection to determine RV volumes. The RV volumes by real-time 3-dimensional echocardiography are well correlated with those of drained in vitro (y = 1.26x - 9.92, r = 0.97, P <.0001, standard error of the estimate = 3.26 mL). For human subjects, the end-diastolic and end-systolic RV volumes were calculated by tracing serial cross-sectional, inclined C scans; functional data were validated by comparing the scans with conventional 2-dimensional echocardiographic indexes of left ventricular stroke volume. CONCLUSIONS: These data indicate that RV volume measurements of excised heart by real-time 3-dimensional echocardiography are accurate and that beat-to-beat RV quantitative measurement applying this imaging method is possible. The new application of real-time 3-dimensional echocardiography presents the opportunity to develop new descriptors of cardiac performance.


Subject(s)
Contrast Media/administration & dosage , Echocardiography, Three-Dimensional , Heart Ventricles/diagnostic imaging , Sodium Chloride , Ventricular Function, Right/physiology , Animals , Dogs , Feasibility Studies , Humans , Injections, Intravenous , Reference Values , Reproducibility of Results , Sodium Chloride/administration & dosage
10.
Biochemistry ; 37(42): 14683-91, 1998 Oct 20.
Article in English | MEDLINE | ID: mdl-9778343

ABSTRACT

Understanding the issue of specificity imposed in the interactions of SH3 domains has largely been addressed in studies investigating the interaction of proline-rich amino acid sequences derived from potential ligands for these domains. Although the interaction with this motif forms an essential platform in the binding of SH3 domains, in many cases little specificity is observed and the difference in affinity for so-called specific and nonspecific proline-rich sequences is not great. Furthermore, the binding interface between an SH3 domain and a protein ligand appears to encompass more interactions than are represented by that involving the proline-rich motif. Here we investigate the issue of specificity from the opposite point of view; namely, how does a ligand recognize different SH3 domains? We present the crystal structure of the unbound SH3 domain from hemopoietic cell kinase (Hck) which is a member of the Src family of tyrosine kinases. This structure reveals that, unlike the structures of other Src kinase SH3 domains, the RT loop region is highly mobile and lacks a network of hydrogen bonds that is elsewhere apparent. The RT loop has been shown to form a major part of the binding interface between SH3 domains and HIV-1 Nef. Thermodynamic data, derived from isothermal titration calorimetry, for the binding of Hck SH3 to HIV-1 Nef show that the binding of Hck (KD = 1.5 microM) is approximately an order of magnitude tighter than those of other Src family kinases that were investigated (Fyn, Lck, and Src). This increase in affinity is attributed to, among other effects, the inherent flexibility in the RT loop which does not require breaking the network of hydrogen bonds to adopt the conformation required for binding.


Subject(s)
Arginine/chemistry , Gene Products, nef/chemistry , HIV-1/chemistry , Threonine/chemistry , src Homology Domains , Amino Acid Sequence , Arginine/metabolism , Crystallization , Crystallography, X-Ray , Gene Products, nef/metabolism , Humans , Models, Molecular , Molecular Sequence Data , Protein Binding , Protein Conformation , Protein-Tyrosine Kinases/chemistry , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins c-hck , Salts , Structure-Activity Relationship , Thermodynamics , Threonine/metabolism , nef Gene Products, Human Immunodeficiency Virus
11.
Eur J Clin Pharmacol ; 54(5): 383-7, 1998 Jul.
Article in English | MEDLINE | ID: mdl-9754980

ABSTRACT

OBJECTIVE: The primary objective was to evaluate the effect of 7 days treatment with nimesulide on bleeding time. Blood coagulation, von Willebrand factor and platelet aggregation ex vivo were investigated as a secondary objective. METHOD: A randomised, double-blind, placebo-controlled, parallel group, single centre study performed on 20 healthy male volunteers who received either placebo or nimesulide 100 mg twice daily for 7 days. Bleeding time, platelet count and platelet aggregation, thromboplastin time (prothrombin time), activated partial thromboplastin time, fibrinogen, Factor VIII:C, vWF:Ag, vWF:RCof and platelet-rich plasma aggregation following stimulation with adenosine 5'-diphosphate, collagen, arachidonic acid, ristocetin, thrombin and thrombin receptor-activating peptide were measured at baseline (day 0), and then 3 h after the first (day 1) and last (day 7) treatment. RESULTS: The bleeding times for all subjects remained within the normal range throughout the study period, with no significant differences between the two treatment groups. There were no significant changes from baseline in platelet aggregation studies or in any of the other haemostasis tests, with no significant differences between the two groups. No clinically significant adverse events were reported or observed. CONCLUSIONS: Daily administration of 200 mg nimesulide for 7 days neither prolongs bleeding time nor modifies any of the other haemostasis variables measured. The lack of interactions with important haemostatic mechanisms suggests that nimesulide may also be used in patients with bleeding problems. This expectation has still to be confirmed by clinical experience.


Subject(s)
Anti-Inflammatory Agents, Non-Steroidal/pharmacology , Hemostasis/drug effects , Sulfonamides/pharmacology , Adult , Anti-Inflammatory Agents, Non-Steroidal/adverse effects , Bleeding Time , Double-Blind Method , Drug Administration Schedule , Humans , Male , Placebos , Platelet Aggregation/drug effects , Sulfonamides/adverse effects , von Willebrand Factor/drug effects , von Willebrand Factor/metabolism
12.
J Biomol NMR ; 11(3): 337-54, 1998 Apr.
Article in English | MEDLINE | ID: mdl-9691281

ABSTRACT

The human oncoprotein p13MTCP1 is coded by the MTCP1 gene, a gene involved in chromosomal translocations associated with T-cell prolymphocytic leukemia, a rare form of human leukemia with a mature T-cell phenotype. The primary sequence of p13MTCP1 is highly and only homologous to that of p14TCL1, a product coded by the gene TCL1 which is also involved in T-cell prolymphocytic leukemia. These two proteins probably represent the first members of a new family of oncogenic proteins. We present the three-dimensional solution structure of the recombinant p13MTCP1 determined by homonuclear proton two-dimensional NMR methods at 600 MHz. After proton resonance assignments, a total of 1253 distance restraints and 64 dihedral restraints were collected. The solution structure of p13MTCP1 is presented as a set of 20 DYANA structures. The rmsd values with respect to the mean structure for the backbone and all heavy atoms for the conformer family are 1.07 +/- 0.19 and 1.71 +/- 0.17 A, when the structured core of the protein (residues 11-103) is considered. The solution structure of p13MTCP1 consists of an orthogonal beta-barrel, composed of eight antiparallel beta-strands which present an original arrangement. The two beta-pleated loops which emerge from this barrel might constitute the interaction surface with a potential molecular partner.


Subject(s)
Nuclear Magnetic Resonance, Biomolecular/methods , Recombinant Proteins/chemistry , Amino Acid Sequence , Humans , Hydrogen Bonding , Models, Molecular , Molecular Sequence Data , Protein Structure, Secondary , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/genetics , Solutions
13.
Biochemistry ; 37(28): 9964-75, 1998 Jul 14.
Article in English | MEDLINE | ID: mdl-9665701

ABSTRACT

Dynamics of the rat alpha-parvalbumin calcium-loaded form have been determined by measurement of 15N nuclear relaxation using proton-detected heteronuclear NMR spectroscopy. The relaxation data were analyzed using spectral density functions and the Lipari-Szabo formalism. The major dynamic features for the rat alpha-parvalbumin calcium-loaded form are (1) the extreme rigidity of the helix-loop-helix EF-hand motifs and the linker segment connecting them, (2) the N and C termini of the protein being restricted in their mobility, (3) a conformational exchange occurring at the kink of helix D, and (4) the residue at relative position 2 in the Ca2+-binding sites having an enhanced mobility. Comparison of the Ca2+-binding EF-hand domains of alpha-parvalbumin-Ca2+, calbindin-Ca2+, and calmodulin-Ca2+ shows that parvalbumin is probably the most rigid of the EF-hand proteins. It also illustrates the dynamical properties which are conserved in the EF-hand domains from different members of this superfamily: (1) a tendency toward higher mobility of NH vectors at relative position 2 in the Ca2+-binding loop, (2) a restricted mobility for the other residues in the binding loop, and (3) an overall rigidity for the helices of EF-hand motifs. The differences in mobility between parvalbumin and the two EF-hand proteins occur mainly at the linker connecting the pair of EF hands and also at the C terminus of the last helix. In parvalbumin-Ca2+, these two regions are characterized by a pronounced rigidity compared to the corresponding more mobile regions in calbindin-Ca2+ and calmodulin-Ca2+.


Subject(s)
Calcium-Binding Proteins/chemistry , Parvalbumins/chemistry , Protein Conformation , Thermodynamics , Amides , Animals , Calcium-Binding Proteins/metabolism , Models, Molecular , Nitrogen Isotopes , Nuclear Magnetic Resonance, Biomolecular , Parvalbumins/metabolism , Protein Structure, Secondary , Protons , Rats
14.
Structure ; 5(10): 1361-72, 1997 Oct 15.
Article in English | MEDLINE | ID: mdl-9351809

ABSTRACT

BACKGROUND: Human immunodeficiency virus (HIV) Nef protein accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src family of kinases. The structures of free Nef and Nef bound to Src homology region 3 (SH3) domain are important for the elucidation of how the affinity and specificity for the Src kinase family SH3 domains are achieved, and also for the development of potential drugs and vaccines against AIDS. RESULTS: We have determined the crystal structures of the conserved core of HIV-1 Nef protein alone and in complex with the wild-type SH3 domain of the p59fyn protein tyrosine kinase (Fyn), at 3.0 A resolution. Comparison of the bound and unbound Nef structures revealed that a proline-rich motif (Pro-x-x-Pro), which is implicated in SH3 binding, is partially disordered in the absence of the binding partner; this motif only fully adopts a left-handed polyproline type II helix conformation upon complex formation with the Fyn SH3 domain. In addition, the structures show how an arginine residue (Arg77) of Nef interacts with Asp 100 of the so-called RT loop within the Fyn SH3 domain, and triggers a hydrogen-bond rearrangement which allows the loop to adapt to complement the Nef surface. The Arg96 residue of the Fyn SH3 domain is specifically accommodated in the same hydrophobic pocket of Nef as the isoleucine residue of a previously described Fyn SH3 (Arg96-->lle) mutant that binds to Nef with higher affinity than the wild type. CONCLUSIONS: The three-dimensional structures support evidence that the Nef-Fyn complex forms in vivo and may have a crucial role in the T cell perturbating action of Nef by altering T cell receptor signaling. The structures of bound and unbound Nef reveal that the multivalency of SH3 binding may be achieved by a ligand induced flexibility in the RT loop. The structures suggest possible targets for the design of inhibitors which specifically block Nef-SH3 interactions.


Subject(s)
Gene Products, nef/chemistry , HIV-1/chemistry , Proto-Oncogene Proteins/chemistry , src Homology Domains , Amino Acid Sequence , Conserved Sequence/genetics , Crystallography, X-Ray , Gene Products, nef/metabolism , Humans , Models, Molecular , Molecular Sequence Data , Peptides/chemistry , Protein Binding , Protein Conformation , Protein Structure, Secondary , Proto-Oncogene Proteins/metabolism , Proto-Oncogene Proteins c-fyn , Receptors, Antigen, T-Cell/metabolism , Sequence Alignment , Signal Transduction , T-Lymphocytes/metabolism , nef Gene Products, Human Immunodeficiency Virus
15.
EMBO J ; 16(16): 5019-29, 1997 Aug 15.
Article in English | MEDLINE | ID: mdl-9305643

ABSTRACT

SacY is the prototype of a family of regulatory proteins able to prevent transcription termination. It interacts with a 29 nucleotide RNA sequence able to fold into a stem-loop structure and partially overlapping with a terminator sequence located in the 5' leader mRNA region of the gene it controls. We show here that the N-terminal fragment of SacY, SacY(1-55), and the corresponding fragments of other members of the family have antiterminator activities with efficiency and specificity identical to those of the full-length proteins. In vitro, this activity correlates with the specific affinity of SacY(1-55) for its RNA target. UV melting experiments demonstrate that SacY(1-55) binding stabilizes the RNA target structure. The NMR solution structure of SacY(1-55) is very similar to that obtained in the crystal (van Tilbeurgh et al., 1997): the peptide is folded as a symmetrical dimer without any structural homology with other RNA-binding domains yet characterized. According to a preliminary NMR analysis of the SacY(1-55)-RNA complex, the protein dimer is not disrupted upon RNA binding and several residues implicated in RNA recognition are located at the edge of the dimer interface. This suggests a new mode of protein-RNA interaction.


Subject(s)
Bacterial Proteins/chemistry , RNA-Binding Proteins/chemistry , Transcription Factors , Amino Acid Sequence , Bacillus subtilis/genetics , Bacillus subtilis/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Chromatography, Gel , Dimerization , Genes, Reporter , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Sequence Data , Nucleic Acid Conformation , Nucleic Acid Denaturation , Protein Conformation , Protein Folding , Protein Structure, Secondary , RNA, Messenger/chemistry , RNA, Messenger/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Recombinant Proteins/chemistry , Sequence Homology, Amino Acid
16.
Proteins ; 28(4): 590-4, 1997 Aug.
Article in English | MEDLINE | ID: mdl-9261875

ABSTRACT

SacY is the antiterminator protein involved in the induction by sucrose of the expression of the levansucrase gene (sacB) of Bacillus subtilis. In the presence of sucrose, SacY is activated and prevents premature termination of transcription by binding to a RNA-antiterminator (RAT) sequence partially overlapping with the terminator sequence. SacY consists of a RNA-binding N-terminal domain, SacY(1-55), and a regulatory domain, SacY(56-280), sensitive to the sucrose concentration. SacY(1-55) is in itself capable of binding to the RAT sequence and preventing termination independently of the sucrose concentration. In this paper we describe the overexpression, the purification, and the crystallization of SacY(1-55). We obtained six different crystal forms, some of them diffracting to high resolution (> 1.5 A). Self rotation function calculations indicated the presence of a dimer in the asymmetric unit, which is in agreement with a proposed oligomeric state in solution as observed by high-resolution NMR measurements. The crystallization of some site-directed cysteine mutants opens the way of solving the structure by multiple isomorphous replacement.


Subject(s)
Bacillus subtilis/chemistry , Bacterial Proteins/chemistry , RNA-Binding Proteins/chemistry , Transcription Factors , Binding Sites , Crystallography, X-Ray , Escherichia coli/metabolism , RNA/metabolism , Recombinant Fusion Proteins/chemistry , Transcription, Genetic
17.
J Mol Biol ; 274(5): 801-15, 1997 Dec 19.
Article in English | MEDLINE | ID: mdl-9405159

ABSTRACT

MTCP1 (for Mature-T-Cell Proliferation) is the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. The three-dimensional solution structure of the human p8(MTCP1) protein encoded by the MTCP1 oncogene was determined by homonuclear proton two-dimensional NMR methods at 600 MHz. After sequence specific assignments, a total of 931 distance restraints and 57 dihedral restraints were collected. The location of the three previously unassigned disulfide bridges was determined from preliminary DIANA structures, using a statistical analysis of intercystinyl distances. The solution structure of p8(MTCP1) is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics using a simulated annealing protocol with the AMBER force field. The r.m.s.d. values with respect to the mean structure for the backbone and all heavy atoms for a family of 30 structures are 0.73(+/-0.28) and 1.17(+/-0.23) A, when the structured core of the protein (residues 5 to 63) is considered. The solution structure of p8(MTCP1) reveals an original scaffold consisting of three alpha helices, associated with a new cysteine motif. Two of the helices are covalently paired by two disulfide bridges, forming an alpha-hairpin which resembles an antiparallel coiled-coil. The third helix is oriented roughly parallel to the plane defined by the alpha-antiparallel motif and its axis forms an angle of approximately 60 degrees with respect to the main axis of this motif.


Subject(s)
Cysteine/chemistry , Protein Conformation , Computer Simulation , Crystallography, X-Ray , Humans , Magnetic Resonance Spectroscopy , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular/methods , Oncogenes , Protein Structure, Secondary , Proto-Oncogene Proteins/chemistry
18.
Protein Sci ; 6(12): 2681-3, 1997 Dec.
Article in English | MEDLINE | ID: mdl-9416624

ABSTRACT

Human immunodeficiency virus Nef protein accelerates virulent progression of AIDS by its interaction with specific cellular proteins involved in cellular activation and signal transduction. Here we report the purification and crystallization of the conserved core of HIV-1LAI Nef protein in the unliganded form and in complex with the wild-type SH3 domain of the P59fyn protein-tyrosine kinase. One-dimensional NMR experiments show that full-length protein and truncated fragment corresponding to the product of HIV-1 protease cleavage have a well-folded compact tertiary structure. The ligand-free HIV-1 Nefcore protein forms cubic crystals belonging to space group P23 with unit cell dimensions of a = b = c = 86.4 A. The Nef-Fyn SH3 cocrystals belong to the space group P6(1)22 or its enantiomorph, P6(5)22, with unit cell dimensions of a = b = 108.2 A and c = 223.7 A. Both crystal forms diffract to a resolution limit of 3.0 A resolution using synchrotron radiation, and are thus suitable for X-ray structure determination.


Subject(s)
Crystallography, X-Ray , Gene Products, nef/chemistry , HIV-1/chemistry , Crystallization , Escherichia coli/genetics , Gene Products, nef/isolation & purification , HIV Protease/metabolism , Light , Magnetic Resonance Spectroscopy , Peptide Fragments/chemistry , Protein Folding , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Scattering, Radiation , nef Gene Products, Human Immunodeficiency Virus
19.
J Biol Chem ; 269(45): 28091-7, 1994 Nov 11.
Article in English | MEDLINE | ID: mdl-7525566

ABSTRACT

Human immunodeficiency virus type 1 reverse transcriptase has subunits of 66 and 51 kDa (p66 and p51, respectively). Structural studies indicate that each subunit consists of common subdomains. The polymerase domain of p66 forms a nucleic acid binding cleft, and, by analogy with a right hand, the subdomains are referred to as fingers, palm, and thumb (Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A., and Steitz, T. A. (1992) Science 256, 1783-1790). Residues 257-266 correspond to a highly conserved region of primary structure among retroviral pol genes. Crystallographic evidence indicates that these residues are in the thumb subdomain and form part of an alpha-helix (alpha H), which interacts with DNA (Jacobo-Molina, A., Ding, J., Nanni, R. G., Clark, A. D., Jr., Lu, X., Tantillo, C., Williams, R. L., Kamer, G., Ferris, A. L., Clark, P., Hizi, A., Hughes, S. H., and Arnold, E. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 6320-6324). To define the role of this region during catalytic cycling, we performed systematic site-directed mutagenesis from position 253 through position 271 by changing each residue, one by one, to alanine. Each mutant protein was expressed and purified, and their substrate-specific activities were surveyed. The results are consistent with alpha H (residues 255-268) of p66 interacting with the template and/or primer strand. The core of alpha H appears to play an important role in template-primer binding (residues Gln-258, Gly-262, and Trp-266), and in protein-protein interactions (residues Val-261 and Leu-264). The periodicity of the effects observed suggest that a segment of one face of alpha H interacts with the template-primer. The lower fidelity observed with alanine mutants of Gly-262 and Trp-266 correlated with an over 200-fold increase in the dissociation rate constant for template-primer relative to wild type enzyme and suggests that enzyme-DNA interactions in the template-primer stem are important fidelity determinants.


Subject(s)
Alanine , HIV-1/enzymology , Protein Structure, Secondary , RNA-Directed DNA Polymerase/chemistry , RNA-Directed DNA Polymerase/metabolism , Amino Acid Sequence , Base Sequence , Codon/genetics , Electrophoresis, Polyacrylamide Gel , HIV Reverse Transcriptase , Macromolecular Substances , Molecular Sequence Data , Mutagenesis, Insertional , Mutagenesis, Site-Directed , Point Mutation , RNA-Directed DNA Polymerase/isolation & purification , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Restriction Mapping , Structure-Activity Relationship
20.
J Magn Reson Imaging ; 4(3): 497-505, 1994.
Article in English | MEDLINE | ID: mdl-7802866

ABSTRACT

A protein-encaged superparamagnetic iron oxide has been developed and characterized by using horse spleen apoferritin as a novel bioreactive environment. The roughly spherical magnetoferritin molecules, 120 A in diameter, are composed of a monocrystalline maghemite or magnetite core 73 A +/- 14 in diameter. Except for the additional presence of iron-rich molecules of higher molecular weight, the appearance and molecular weight (450 kd) of magnetoferritin are identical to that of natural ferritin; the molecules are externally indistinguishable from their precursor, with a pI (isoelectric point) in the range 4.3-4.6. The measured magnetic moment of the superparamagnetic cores is 13,200 Bohr magnetons per molecule, with T1 and T2 relaxivities (r1 and r2) of 8 and 175 L.mmol-1 (Fe).sec-1, respectively, at body temperature and clinical field strengths. The unusually high r2/r1 ratio of 22 is thought to arise from ideal core composition, with no evidence of crystalline paramagnetic inclusions. T2 relaxation enhancement can be well correlated to the field-dependent molecular magnetization, as given by the Langevin magnetization function, raised to a power in the range 1.4-1.6. With its nanodimensional biomimetic protein cage as a rigid, convenient matrix for complexing a plethora of bioactive substances, magnetoferritin may provide a novel template for specific targeting of selected cellular sites.


Subject(s)
Contrast Media , Magnetic Resonance Imaging , Animals , Apoferritins/analogs & derivatives , Apoferritins/chemical synthesis , Apoferritins/chemistry , Contrast Media/chemical synthesis , Contrast Media/chemistry , Dextrans , Ferrosoferric Oxide , Horses , Iron/chemistry , Magnetite Nanoparticles , Oxides/chemical synthesis , Oxides/chemistry
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