Biomedical subjects

C Bustamante

Publications and source records attributed to C Bustamante.

At least 19 recordsLinked to original sources

PubMed2006

Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers.

When mixed together, DNA and polyaminoamide dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension curves (FECs). A characteristic force plateau (around 10 pN) and hysteresis between the pulling and relaxation cycles are observed for different dendrimer sizes, indicating the existence of a first-order transition between two phases (condensed and extended) of the fiber. Upon salt variation FECs change noticeably confirming that electrostatic forces drive the condensation transition. We propose a simple model for the decondensing transition that qualitatively reproduces the FECs and which is confirmed by atomic force microscopy images.

Bacteriophage lambda↗

PubMed2005

Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies.

Atomic force microscopes and optical tweezers are widely used to probe the mechanical properties of individual molecules and molecular interactions, by exerting mechanical forces that induce transitions such as unfolding or dissociation. These transitions often occur under nonequilibrium conditions and are associated with hysteresis effects-features usually taken to preclude the extraction of equilibrium information from the experimental data. But fluctuation theorems allow us to relate the work along nonequilibrium trajectories to thermodynamic free-energy differences. They have been shown to be applicable to single-molecule force measurements and have already provided information on the folding free energy of a RNA hairpin. Here we show that the Crooks fluctuation theorem can be used to determine folding free energies for folding and unfolding processes occurring in weak as well as strong nonequilibrium regimes, thereby providing a test of its validity under such conditions. We use optical tweezers to measure repeatedly the mechanical work associated with the unfolding and refolding of a small RNA hairpin and an RNA three-helix junction. The resultant work distributions are then analysed according to the theorem and allow us to determine the difference in folding free energy between an RNA molecule and a mutant differing only by one base pair, and the thermodynamic stabilizing effect of magnesium ions on the RNA structure.

Base Pairing↗

PubMed2002

A two-state kinetic model for the unfolding of single molecules by mechanical force.

We investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states) separated by an intermediate barrier. We compute the probability distribution for the dissipated work and give analytical expressions for the average and variance of the distribution. To first order, the amount of dissipated work is directly proportional to the rate of application of force (the loading rate) and to the relaxation time of the molecule. The model yields estimates for parameters that characterize the unfolding kinetics under force in agreement with those obtained in recent experimental results. We obtain a general equation for the minimum number of repeated experiments needed to obtain an equilibrium free energy, to within k(B)T, from nonequilibrium experiments by using the Jarzynski formula. The number of irreversible experiments grows exponentially with the ratio of the average dissipated work, W(dis) to k(B)T.

Biomechanical Phenomena↗

PubMed2002

[Neurohagiography. Lamberto Caesaraugustanus, the cephalophoric: holy patron of Spanish neurology?].

Until now Neurology has lacked a patron saint who, taking the most advantage of the rich cultural tradition inherited from our past and independently of the religious ideology of each one, can be helpful approach in the neurologist figure to different people. An Ad Hoc Committee from the Neurology History Study Group of the SEN has researched the medical hagiography with any kind of neurological relationship (neurohagiography), in order to make a hagiography study of every saint related to our speciality, with the added luck of proposing a patron for Neurology with hispanic origin. In this pioneer study of historiographic research different documents related with the medical hagiography have been studied, especially the Index ac Status Causarum, and information coming from different national ecclesiastic archives. A total of 342 saints share the patronage of 137 diseases, of which a 27,7% are related in some way to Neurology. Headache constitutes the prime cause of the invocations, with 20 saints. Another 11 saints plead for epilepsy; to these we also must add another six for so called possessed patients. Therefore, two of the three main causes of invocation (headache, fever and epilepsy) come up to chronic processes. Of all the saints with a hispanic origin candidates to the patronage of the neurologists San Lamberto Caesaraugustanus stands out, who died in the year 303 during Diocletian persecution. Belonging to the selected standing of "cephalophoric martyrs" (those beheahed who carry their own head in their hands), he was able to walk an important distance (about six kilometres) with his head split from the body, a fact only understood as a suprahuman phenomenon thanks to which he has becomes the brain transplant pioneer.

History, 16th Century↗

PubMed2001

The bacteriophage straight phi29 portal motor can package DNA against a large internal force.

As part of the viral infection cycle, viruses must package their newly replicated genomes for delivery to other host cells. Bacteriophage straight phi29 packages its 6.6-microm long, double-stranded DNA into a 42 x 54 nm capsid by means of a portal complex that hydrolyses ATP. This process is remarkable because entropic, electrostatic and bending energies of the DNA must be overcome to package the DNA to near-crystalline density. Here we use optical tweezers to pull on single DNA molecules as they are packaged, thus demonstrating that the portal complex is a force-generating motor. This motor can work against loads of up to 57 pN on average, making it one of the strongest molecular motors reported to date. Movements of over 5 microm are observed, indicating high processivity. Pauses and slips also occur, particularly at higher forces. We establish the force-velocity relationship of the motor and find that the rate-limiting step of the motor's cycle is force dependent even at low loads. Notably, the packaging rate decreases as the prohead is filled, indicating that an internal force builds up to approximately 50 pN owing to DNA confinement. Our data suggest that this force may be available for initiating the ejection of the DNA from the capsid during infection.

Bacillus Phages↗

PubMed2001

Effect of poly(ADP-ribosyl)ation and Mg2+ ions on chromatin structure revealed by scanning force microscopy.

Poly(ADP-ribosyl)ation of nuclear proteins is responsible for major changes in the high-order chromatin structure. The effects of this post-translation modification on nuclear architecture were examined at different Mg2+ concentrations using scanning force microscopy. A quantitative analysis of the internucleosomal distance, the width, and the volume of chromatin fibers imaged in tapping mode reveals that poly(ADP-ribosyl)ation induces a complete relaxation and decondensation of the chromatin structure. Our data, on the center-to-center distance between adjacent nucleosomes and on the fiber width, indicate that the poly(ADP-ribosyl)ated fibers remain significantly decondensed even in the presence of Mg2+. Our results also show that the Mg2+ assumes an important role in the folding of chromatin structure, but Mg2+ is not able to restore the native feature of chromatin, when the fibers are depleted of H1/H5 histones. The combined effect of post-translation modification and cation ions on the chromatin structure shows that poly(ADP-ribosyl)ation could promote accessibility to DNA even in those nuclear processes that require Mg2+.

Chromatin↗

PubMed2001

Reversible unfolding of single RNA molecules by mechanical force.

Here we use mechanical force to induce the unfolding and refolding of single RNA molecules: a simple RNA hairpin, a molecule containing a three-helix junction, and the P5abc domain of the Tetrahymena thermophila ribozyme. All three molecules (P5abc only in the absence of Mg2+) can be mechanically unfolded at equilibrium, and when kept at constant force within a critical force range, are bi-stable and hop between folded and unfolded states. We determine the force-dependent equilibrium constants for folding/unfolding these single RNA molecules and the positions of their transition states along the reaction coordinate.

Animals↗

PubMed2001

Mechanical fatigue in repetitively stretched single molecules of titin.

Relaxed striated muscle cells exhibit mechanical fatigue when exposed to repeated stretch and release cycles. To understand the molecular basis of such mechanical fatigue, single molecules of the giant filamentous protein titin, which is the main determinant of sarcomeric elasticity, were repetitively stretched and released while their force response was characterized with optical tweezers. During repeated stretch-release cycles titin becomes mechanically worn out in a process we call molecular fatigue. The process is characterized by a progressive shift of the stretch-force curve toward increasing end-to-end lengths, indicating that repeated mechanical cycles increase titin's effective contour length. Molecular fatigue occurs only in a restricted force range (0-25 pN) during the initial part of the stretch half-cycle, whereas the rest of the force response is repeated from one mechanical cycle to the other. Protein-folding models fail to explain molecular fatigue on the basis of an incomplete refolding of titin's globular domains. Rather, the process apparently derives from the formation of labile nonspecific bonds cross-linking various sites along a pre-unfolded titin segment. Because titin's molecular fatigue occurs in a physiologically relevant force range, the process may play an important role in dynamically adjusting muscle's response to the recent history of mechanical perturbations.

Animals↗

PubMed2001

The physics of molecular motors.

Molecular motors convert chemical energy into mechanical force and movement. Operating at energies just above those of the thermal bath, these motors experience large fluctuations, and their physical description must be necessarily stochastic. Here, motor operation is described as a biased diffusion on a potential energy surface defined by the interactions of the motor with its track and its fuel. These ideas are illustrated with a model of the rotary movement of the F(o) motor.

Animals↗

PubMed2001

[Prospective follow-up of a HIV infected population with and without access to antiretroviral therapy: impact of survival and complications].

BACKGROUND: Three-drug antiretroviral therapy (ART-3) has reduced complications and improved survival in HIV+ patients. The Chilean Public Health System began dual therapy (ART-2) in 1997, covering approximately 40% of patients in need. AIM: To report the results of a follow-up of patients with and without access to ART in a Chilean public hospital. PATIENT AND METHODS: Prospective follow-up of patients with ART-2 and 3 (cases) and patients with no access to ART (controls). All patients needed ART but it was available to a minority of them. Selection for ART was at random. Follow-up was between 6-24 months (11/96 to 3/99). Basal and periodic clinical and laboratory parameters were determined. Mortality and occurrence of new AIDS-defining events (ADE) were compared statistically using chi square. RESULTS: One hundred and fifty cases (106 ART2, 28 ART3 and 16 ART2 expanded to ART3) and 166 controls were studied. Basal parameters were similar except prior ART (32.7 and 18.7% in cases and controls respectively). Close to 1/3 patients had AIDS. Cases had a mean follow up of 527 days; controls, 478. Six cases (4%) (5 in ART-2) and 17 controls (10%) died. Mortality x 100/pts/yr was 2.7 in cases and 7.7 in controls, p < 0.05. ADE per 100/pts/yr was 21 in cases (24.4 in ART2, 15.1 in TAR3) and 54.5 in controls, p < 0.05. Cases had a reduction of: esophageal candidiasis (84%), tuberculosis (75%), cryptococcosis and toxoplasmosis (66%), P carinii pneumonia (55%) and bacterial pneumonia (46%) and they had fewer hospitalizations (73%). Late assessment: 70 of 101 ART-2 patients had changed to ART-3 (1 death); 22 of 101 kept original ART-2 (12 dead, 10 alive), 39 of 43 ART-3 patients were alive and 1 died. CONCLUSIONS: Short-term ART-2 and 3 significantly reduced mortality (60% and 73%) ADE (65% and 76% respectively) and hospitalizations. Benefits of ART-2 were short lived. Resource-constrained countries cannot depend on weaker than standard ART for proper care of people with HIV disease.

Adult↗

PubMed2000

Positive torsional strain causes the formation of a four-way junction at replication forks.

The advance of a DNA replication fork requires an unwinding of the parental double helix. This in turn creates a positive superhelical stress, a (+)-DeltaLk, that must be relaxed by topoisomerases for replication to proceed. Surprisingly, partially replicated plasmids with a (+)-DeltaLk were not supercoiled nor were the replicated arms interwound in precatenanes. The electrophoretic mobility of these molecules indicated that they have no net writhe. Instead, the (+)-DeltaLk is absorbed by a regression of the replication fork. As the parental DNA strands re-anneal, the resultant displaced daughter strands base pair to each other to form a four-way junction at the replication fork, which is locally identical to a Holliday junction in recombination. We showed by restriction endonuclease digestion that the junction can form at either the terminus or the origin of replication and we visualized the structure with scanning force microscopy. We discuss possible physiological implications of the junction for stalled replication in vivo.

DNA Replication↗

PubMed2000

Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase.

Using an optical-trap/flow-control video microscopy technique, we followed transcription by single molecules of Escherichia coli RNA polymerase in real time over long template distances. These studies reveal that RNA polymerase molecules possess different intrinsic transcription rates and different propensities to pause and stop. The data also show that reversible pausing is a kinetic intermediate between normal elongation and the arrested state. The conformational metastability of RNA polymerase revealed by this single-molecule study of transcription has direct implications for the mechanisms of gene regulation in both bacteria and eukaryotes.

DNA, Bacterial↗

PubMed2000

Single-molecule studies of the effect of template tension on T7 DNA polymerase activity.

T7 DNA polymerase catalyses DNA replication in vitro at rates of more than 100 bases per second and has a 3'-->5' exonuclease (nucleotide removing) activity at a separate active site. This enzyme possesses a 'right hand' shape which is common to most polymerases with fingers, palm and thumb domains. The rate-limiting step for replication is thought to involve a conformational change between an 'open fingers' state in which the active site samples nucleotides, and a 'closed' state in which nucleotide incorporation occurs. DNA polymerase must function as a molecular motor converting chemical energy into mechanical force as it moves over the template. Here we show, using a single-molecule assay based on the differential elasticity of single-stranded and double-stranded DNA, that mechanical force is generated during the rate-limiting step and that the motor can work against a maximum template tension of approximately 34 pN. Estimates of the mechanical and entropic work done by the enzyme show that T7 DNA polymerase organizes two template bases in the polymerization site during each catalytic cycle. We also find a force-induced 100-fold increase in exonucleolysis above 40 pN.

Bacteriophage T7↗

PubMed2000

Pulling chromatin fibers: computer simulations of direct physical micromanipulations.

A low-resolution molecular model, which combines the known mechanical properties of protein-free DNA with the accumulating picture of chromatosome structure, has been developed to account for the stretching of single chromatin fibers by an imposed external force. Force-extension characteristics of sets of chains accumulated by Monte Carlo sampling are consistent with recently observed findings in the non-destructive regime (<20 pN imposed force), where the structure of the chromatosome remains intact. The correspondence between simulation and the relaxation phase of the experiment limits the equilibrium entry-exit angle of linker DNA on the chromatosome to W=50(+/-10) degrees and the effective DNA linker length to L(eff)=40(+/-5) bp. The computed force-extension characteristics are relatively insensitive to other parameters of the model, precluding their accurate estimation. The introduction of an attractive potential between closely spaced nucleosomes reproduces the added initial resistance of single fibers to extension at high salt conditions. The consideration of elastic linkers also improves the fitting of assorted classical measurements of unstressed chromatin structure in solution. The overall picture of chromatin that emerges is an irregular, fluctuating, three-dimensional, zig-zag structure with intact, mechanically stable chromatosome units and deformable linkers. The modeled fiber undergoes large-scale configurational rearrangements without significant perturbation of the constituent chromatosome beads, collapsing into a highly condensed form in response to small (<2kT) inter-nucleosomal attractions.

Calibration↗

PubMed2000

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure.

Single chicken erythrocyte chromatin fibers were stretched and released at room temperature with force-measuring laser tweezers. In low ionic strength, the stretch-release curves reveal a process of continuous deformation with little or no internucleosomal attraction. A persistence length of 30 nm and a stretch modulus of approximately 5 pN is determined for the fibers. At forces of 20 pN and higher, the fibers are modified irreversibly, probably through the mechanical removal of the histone cores from native chromatin. In 40-150 mM NaCl, a distinctive condensation-decondensation transition appears between 5 and 6 pN, corresponding to an internucleosomal attraction energy of approximately 2.0 kcal/mol per nucleosome. Thus, in physiological ionic strength the fibers possess a dynamic structure in which the fiber locally interconverting between "open" and "closed" states because of thermal fluctuations.

Animals↗

PubMed2000

Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme.

Recent advances in single molecule manipulation methods offer a novel approach to investigating the protein folding problem. These studies usually are done on molecules that are naturally organized as linear arrays of globular domains. To extend these techniques to study proteins that normally exist as monomers, we have developed a method of synthesizing polymers of protein molecules in the solid state. By introducing cysteines at locations where bacteriophage T4 lysozyme molecules contact each other in a crystal and taking advantage of the alignment provided by the lattice, we have obtained polymers of defined polarity up to 25 molecules long that retain enzymatic activity. These polymers then were manipulated mechanically by using a modified scanning force microscope to characterize the force-induced reversible unfolding of the individual lysozyme molecules. This approach should be general and adaptable to many other proteins with known crystal structures. For T4 lysozyme, the force required to unfold the monomers was 64 +/- 16 pN at the pulling speed used. Refolding occurred within 1 sec of relaxation with an efficiency close to 100%. Analysis of the force versus extension curves suggests that the mechanical unfolding transition follows a two-state model. The unfolding forces determined in 1 M guanidine hydrochloride indicate that in these conditions the activation barrier for unfolding is reduced by 2 kcal/mol.

Bacteriophage T4↗

PubMed2000

Mechanical manipulation of single titin molecules with laser tweezers.

Titin (also known as connectin) is a giant filamentous polypeptide of multi-domain construction spanning between the Z- and M-lines of the vertebrate muscle sarcomere. The molecule is significant in maintaining sarcomeric structural integrity and generating passive muscle force via its elastic properties. Here we summarize our efforts to characterize titin's elastic properties by manipulating single molecules with force-measuring laser tweezers. The titin molecules can be described as an entropic spring in which domain unfolding occurs at high forces during stretch and refolding at low forces during release. Statistical analysis of a large number (> 500) of stretch-release experiments and comparison of experimental data with the predictions of the wormlike chain theory permit the estimation of unfolded titin's mean persistence length as 16.86 A (+/- 0.11 SD). The slow rates of unfolding and refolding compared with the rates of stretch and release, respectively, result in a state of non-equilibrium and the display of force hysteresis. Folding kinetics as the source of non-equilibrium is directly demonstrated here by the abolishment of force hysteresis in the presence of chemical denaturant. Experimental observations were well simulated by superimposing a simple domain folding kinetics model on the wormlike chain behavior of titin and considering the characteristics of the compliant laser trap. The original video presentation of this paper may be viewed on the web at http:¿www.pote.hu/mm/prezentacio/mkpres/++ +mkpres.htm.

Animals↗

PubMed2000

An integrated laser trap/flow control video microscope for the study of single biomolecules.

We have developed an integrated laser trap/flow control video microscope for mechanical manipulation of single biopolymers. The instrument is automated to maximize experimental throughput. A single-beam optical trap capable of trapping micron-scale polystyrene beads in the middle of a 200-microm-deep microchamber is used, making it possible to insert a micropipette inside this chamber to hold a second bead by suction. Together, these beads function as easily exchangeable surfaces between which macromolecules of interest can be attached. A computer-controlled flow system is used to exchange the liquid in the chamber and to establish a flow rate with high precision. The flow and the optical trap can be used to exert forces on the beads, the displacements of which can be measured either by video microscopy or by laser deflection. To test the performance of this instrument, individual biotinylated DNA molecules were assembled between two streptavidin beads, and the DNA elasticity was characterized using both laser trap and flow forces. DNA extension under varying forces was measured by video microscopy. The combination of the flow system and video microscopy is a versatile design that is particularly useful for the study of systems susceptible to laser-induced damage. This capability was demonstrated by following the translocation of transcribing RNA polymerase up to 650 s.

Calibration↗