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Biomedical subjects

R Lavery

Publications and source records attributed to R Lavery.

At least 19 recordsLinked to original sources
PubMed1999

Modeling DNA deformations induced by minor groove binding proteins.

Molecular modeling is used to demonstrate that the major structural deformations of DNA caused by four different minor groove binding proteins, TBP, SRY, LEF-1, and PurR, can all be mimicked by stretching the double helix between two 3'-phosphate groups flanking the binding region. This deformation reproduces the widening of the minor groove and the overall bending and unwinding of DNA caused by protein binding. It also reproduces the principal kinks associated with partially intercalated amino acid side chains, observed with such interactions. In addition, when protein binding involves a local transition to an A-like conformation, phosphate neutralization, via the formation of protein-DNA salt bridges, appears to favor the resulting deformation.

Base Sequence↗
PubMed1999

Unraveling proteins: a molecular mechanics study.

An internal coordinate molecular mechanics study of unfolding peptide chains by external stretching has been carried out to predict the type of force spectra that may be expected from single-molecule manipulation experiments currently being prepared. Rather than modeling the stretching of a given protein, we have looked at the behavior of simple secondary structure elements (alpha-helix, beta-ribbon, and interacting alpha-helices) to estimate the magnitude of the forces involved in their unfolding or separation and the dependence of these forces on the way pulling is carried out as well as on the length of the structural elements. The results point to a hierarchy of forces covering a surprisingly large range and to important orientational effects in the response to external stress.

Biophysical Phenomena↗
PubMed1999

Collective variable modelling of nucleic acids.

Collective variable models continue to contribute to our knowledge of nucleic acids. The past year has seen considerable progress both in modelling sequence-dependent effects on nucleic acid conformation and in understanding how proteins or external stresses influence nucleic acid structure. Algorithmic developments have also allowed collective models to be applied to studies of thermal fluctuations and dynamics. For larger systems, models with varying degrees of resolution are being refined and applied to nucleic acids containing hundreds or thousands of nucleotides.

Algorithms↗
PubMed1999

Prospective randomized trial of thoracostomy removal algorithms.

INTRODUCTION: The preferred chest tube (CT) removal algorithm has not yet been established. The purpose of this study was to determine which technique, water seal or suction, allowed for shorter CT duration. In addition, the recurrent pneumothorax (PTX) rate, the need for CT reinsertion, and the total number of chest x-ray films (CXR) were determined. METHODS: Prospective randomized trial of 205 trauma patients, older than 15 years of age, requiring tube thoracostomy for blunt and penetrating trauma. Patients requiring mechanical ventilation more than 24 hours were excluded from the study. Informed consent was obtained from all patients. Chest tubes were randomized for removal when output was less than 150 mL/24 hours, CXR revealed no significant PTX, and no air leak was present. Patients in the water seal group were disconnected from low wall suction and a CXR was obtained 6 to 8 hours later. Chest tubes in the no water seal group were disconnected from wall suction and pulled immediately. All tubes were removed by using standard protocol with patients at maximal inspiratory effort. A follow-up CXR was obtained after removal. RESULTS: Of the 205 patients, 93 patients (45 %) were randomized to the water seal group and 112 patients (54%) to the no water seal group. Four patients in the water seal group developed a PTX before CT removal and were considered treatment failures. After CT removal, repeat PTX was seen in 13 patients in the water seal group and in 9 patients in the no water seal group. However, seven patients in the no water seal group required CT reinsertion compared with one in the water seal group (p<0.05). Average number of CXR in the water seal group was 6.5 compared with 5.5 radiographs in the no water seal group. There was no difference in chest tube duration or hospital length of stay between groups for either all patients or only those patients with isolated chest injuries. Patients who required another CT had a hospital length of stay twice that of patients who did not. CONCLUSIONS: It is possible that patients in the no water seal group did not have sufficient time for a possible PTX to evolve, which resulted in a larger and more significant PTX requiring another CT. Although there was no difference in chest tube duration between the no water seal and water seal groups, a short trial of water seal appears to allow occult air leaks to become clinically apparent and reduces the need for another CT.

Adult↗
PubMed1998

Stretched and overwound DNA forms a Pauling-like structure with exposed bases.

We investigate structural transitions within a single stretched and supercoiled DNA molecule. With negative supercoiling, for a stretching force >0.3 pN, we observe the coexistence of B-DNA and denatured DNA from sigma approximately -0.015 down to sigma = -1. Surprisingly, for positively supercoiled DNA (sigma > +0.037) stretched by 3 pN, we observe a similar coexistence of B-DNA and a new, highly twisted structure. Experimental data and molecular modeling suggest that this structure has approximately 2.62 bases per turn and an extension 75% larger than B-DNA. This structure has tightly interwound phosphate backbones and exposed bases in common with Pauling's early DNA structure [Pauling, L. & Corey, R. B. (1953), Proc. Natl. Acad. Sci. USA 39, 84-97] and an unusual structure proposed for the Pf1 bacteriophage [Liu, D. J. & Day, L. A. (1994) Science 265, 671-674].

Antibodies↗
PubMed1998

Role of interleukin 8 in the genesis of acute respiratory distress syndrome through an effect on neutrophil apoptosis.

OBJECTIVE: To evaluate the role of interleukin 8 (IL-8) in the regulation of neutrophil (PMN) apoptosis in normal plasma and plasma from patients with early, fulminant acute respiratory distress syndrome (ARDS). DESIGN: Experimental study using cultured human PMNs. SETTING: University hospital, level I trauma center. PARTICIPANTS: Plasma was obtained from 6 patients with early, fulminant posttraumatic ARDS (mean Injury Severity Score, 26). All samples were drawn within 24 hours after injury. Plasma was also taken from 13 healthy control subjects. These controls were also used as sources of PMNs. MAIN OUTCOME MEASURES: Effect of early, fulminant ARDS and normal plasma on spontaneous apoptosis, CD16, and CD11-b expression in PMNs in vitro; levels of IL-8 in plasma; correlation of extracellular IL-8 concentration with rate of PMN apoptosis; and effect of IL-8 blockade on PMN apoptosis, CD16, and CD11-b expression in ARDS and normal plasma. RESULTS: Plasma from patients with early, fulminant ARDS inhibited spontaneous PMN apoptosis at 24 hours (35%+/-5% vs 54%+/-5%; P=.01). Neither CD16 nor CD1l-b differed significantly between the 2 groups. The mean plasma level of IL-8 in patients with early, fulminant ARDS was 359+/-161 pg/mL vs 3.0+/-0.4 pg/mL in healthy controls (P<.05). Interleukin 8 inhibited apoptosis in plasma-free medium at low doses (1-50 pg/mL) but had no significant effect at higher doses (100-5000 pg/mL) (P<.05). Interleukin 8 blockade with monoclonal antibody suppressed apoptosis in normal plasma (28%+/-5% with monoclonal antibody vs 51%+/-5% without monoclonal antibody; P=.008) but not in plasma from patients with early, fulminant ARDS (29%+/-5% with monoclonal antibody vs 34%+/-6% without monoclonal antibody; P=.67). It had no effect on CD16 or CD11-b expression in either plasma. CONCLUSIONS: Plasma from patients with early, fulminant ARDS contains soluble factors that inhibit PMN apoptosis in vitro. Low levels of IL-8 inhibit PMN apoptosis in normal plasma. Although plasma levels of IL-8 are markedly elevated in early, fulminant ARDS, IL-8 is not directly responsible for the antiapoptotic effect of plasma from patients with early, fulminant ARDS.

Apoptosis↗
PubMed1998

Sequence-dependent dynamics of TATA-Box binding sites.

We have carried out two nanosecond-length molecular dynamics simulations on a DNA oligomer, d(GCGTAAAAAAAACGC)2, which contains a weak binding site for the TATA-box binding protein. An analysis of the resulting trajectories shows that this oligomer behaves differently from a related oligomer [d(GCGTATATAAAACGC)2] studied earlier using the same protocol (Flatters, D., M. Young, D. L. Beveridge, and R. Lavery. 1997. Conformational properties of the TATA-box binding sequence of DNA. J. Biomol. Struct. & Dyn. 14:757-765), and which contains a strong binding site for the same protein. The two basepair mutations that relate these oligomers lead to significant changes in time-averaged structure and in dynamic behavior, which extend over entire length of the oligomer and appear to be compatible with the experimentally observed decrease of binding and functional activity. These results suggest that molecular dynamics simulations, taking into account explicit solvent and counterions, and avoiding the truncation of electrostatic interactions, are a powerful tool for investigating the indirect aspects of protein-nucleic acid recognition.

Base Sequence↗
PubMed1998

Ureteral trauma: preoperative studies neither predict injury nor prevent missed injuries.

BACKGROUND: Ureteral injuries are uncommon, and the necessity, accuracy, and optimal use of perioperative testing remains unknown. Delays in diagnosis have also been associated with significant morbidity, including loss of renal function. STUDY DESIGN: The records of all patients (n = 20) admitted with ureteral injuries to two Level I trauma centers during a 5-year period were reviewed. Data collected included patient demographics, mechanism of injury, degree of associated injuries, and presence of gross or microscopic hematuria. The use of any pre- or intraoperative testing was specifically noted. The location of the ureteral injury was obtained from the operative notes. The morbidity and mortality associated with ureteral injuries in the primarily diagnosed and the delayed groups were assessed. Presenting signs and symptoms, diagnostic testing, and the urologic management of the patients in the delayed group were reviewed. RESULTS: All patients were men whose ages ranged from 15 to 72 years, with a mean age of 29. The mechanisms of injury were gunshot wounds in 15, stab wounds in 4, and blunt vehicular trauma in 1. Excluding other urologic injuries, the incidence of hematuria related to the ureteral injury alone was 53%. A total of 10 pre- and intraoperative studies were performed, only 2 demonstrated the ureteral injury. Seventeen patients had their injuries diagnosed primarily. In this group, the ureter was repaired by suturing and stenting in 12, suturing without a stent in 1 and ureterocystostomy in 4. Delayed diagnosis of their ureteral injuries occurred in three patients. All three missed injuries occurred in the upper portion of the left ureter. All ureters were successfully repaired. There were no mortalities in this group, nor did any patient require a nephrectomy. CONCLUSIONS: Direct visualization of the injury is the best and most accurate diagnostic modality in ureteral trauma. These results reinforce that a thorough exploration of all retroperitoneal hematomas after penetrating trauma remain an integral part of the total abdominal exploration for trauma.

Abdominal Injuries↗
PubMed1998

A model for parallel triple helix formation by RecA: single-single association with a homologous duplex via the minor groove.

The nucleoproteic filaments of RecA polymerized on single stranded DNA are able to integrate double stranded DNA in a coaxial arrangement (with DNA stretched by a factor 1.5), to recognize homologous sequences in the duplex and to perform strand exchange between the single stranded and double stranded molecules. While experimental results favor the hypothesis of an invasion of the minor groove of the duplex by the single strand, parallel minor groove triple helices have never been isolated or even modeled, the minor groove offering little space for a third strand to interact. Based on an internal coordinate modeling study, we show here that such a structure is perfectly conceivable when the two interacting oligomers are stretched by a factor 1.5, in order to open the minor groove of the duplex. The model helix presents characteristics that coincide with known experimental data on unwinding, base pair inclination and inter-proton distances. Moreover, we show that extension and unwinding stabilize the triple helix. New patterns of triplet interaction via the minor groove are presented.

Computer Simulation↗
PubMed1998

Modeling the mechanics of a DNA oligomer.

DNA stretching and strand separation have been studied by molecular mechanics using an oligomer which has been the subject of nanomanipulation experiments (Noy et al., Chem. Biol. 4, 519, 1997). Adiabatic mapping of conformational energy carried out as a function of stretching leads to force/extension curves in good correlation with the experimental results. Other types of deformation are also modeled and compared with the experimental results obtained on polymeric DNA. The results highlight overall similarities, but point to thermodynamic differences and also to local base sequence effects which can be expected to play an important role at the level of biologically induced structural deformations.

Computer Simulation↗
PubMed1997

Local DNA stretching mimics the distortion caused by the TATA box-binding protein.

X-ray structures of the TATA box-binding protein complexed with its DNA target show that the nucleic acid is severely bent away from the protein and also strongly unwound. We have used molecular mechanics and energy mapping to understand how such an unusual conformation can be induced. The results show that simple deformation pathways involving local stretching or unwinding of DNA reproduce many features of the experimental structure. Notably, kinked junctions with the flanking B-DNA regions occur without the need for any specific local

DNA↗
PubMed1997

Unusual DNA conformations.

DNA is on the move across conformational space. Duplexes diversity and, joined by triplexes, quadruplexes, loops, bulges and multiarmed junctions, open the route to a bewildering array of increasingly complex conformations. In addition to this structural growth, DNA has come under increasing scrutiny thanks to the development of chemical and physical techniques for deforming its conformation and probing its properties. These investigations help us to learn more about the mechanics and the activity of this remarkably versatile macromolecule.

DNA↗
PubMed1997

Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: an internal coordinate molecular modeling study.

A trans-diamminedichloroplatinum(II) (trans-DDP) intrastrand adduct within the sequence d(TCTG*TG*TC).d(GACACAGA) (where G* represents a platinated guanine) is modeled on the basis of qualitative experimental data concerning global unwinding and curvature as well as information on base pairing. Modeling is performed using the internal coordinate JUMNA program, specific to nucleic acids, and modified to include the possibility of covalently bound ligands. Calibration of the energy functions representing the Pt-N7 bond with guanine is described. The platinum atom and the platinum-nitrogen bonds are parameterized for use in the Hückel Del Re method to calculate monopoles at each atom. These monopoles are consistent with the Flex force field included in Jumna. By developing an appropriate minimization protocol we are able to generate stable, distorted three-dimensional structures compatible with the experimental data and including an unusually high global unwinding. No a priori geometric assumptions are made in generating these structures.

Algorithms↗
PubMed1997

Conformational properties of the TATA-box binding sequence of DNA.

Nanosecond scale molecular dynamics simulations in water demonstrate that the DNA oligomer, GCGTATATAAAACGC, which contains a target site for the TATA-box binding protein (TBP), has an intrinsic preference to adopt an A-like conformation in the region of the TATA-box and undergoes bending related to that seen within in the TBP complex. This result is obtained from two independent simulations using different starting structures. In line with earlier suggestions of Guzikevich-Guerstein and Shakked, these simulations imply that an A-DNA conformation may be an important intermediate step in forming the strongly distorted DNA observed within the crystallographically determined complex with TBP. These results also support modeling studies by Lebrun et al. which suggest that the TBP binding mechanism can be broken down into a backbone transition to an A-like form coupled with a mechanical distortion which locally stretches and unwinds the DNA.

Binding Sites↗
PubMed1996

Modelling extreme stretching of DNA.

Molecular modelling with Jumna is used to study extreme stretching of the DNA double helix. The results, which correlate well with recent nanomanipulation experiments, show how the double helix can be extended to twice its normal length before its base pairs break. Depending on the way the duplex is stretched two types of conformation can occur, either an unwound flat ribbon or a narrow fibre with negatively inclined base pairs. The energetics of both types of deformation are similar and existing structures show that at least the flat ribbon form can exist locally under biological conditions.

Base Sequence↗
PubMed1996

Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature.

The molecular modelling program JUMNA has been used to investigate the origins of the strikingly different curvature of the two sequences, (A4T4NN)n and (T4A4NN)n. Gel electrophoresis and cyclisation studies have shown that only the former of these two sequences is significantly curved. By developing novel superhelical symmetry constraints we were able to study the energetic and structural aspects of polymeric DNA having a controlled curvature. The results obtained (which do not take into account specific hydration effects) correlate well with the experimental data and offer a molecular level explanation of curvature. Although curvature is found to be initiated by specific dinucleotide junctions, deformations spread to surrounding dinucleotide steps and, moreover, sequence effects beyond the dinucleotide level are observed.

Base Sequence↗
PubMed1996

DNA: an extensible molecule.

The force-displacement response of a single duplex DNA molecule was measured. The force saturates at a plateau around 70 piconewtons, which ends when the DNA has been stretched about 1.7 times its contour length. This behavior reveals a highly cooperative transition to a state here termed S-DNA. Addition of an intercalator suppresses this transition. Molecular modeling of the process also yields a force plateau and suggests a structure for the extended form. These results may shed light on biological processes involving DNA extension and open the route for mechanical studies on individual molecules in a previously unexplored range.

Chemical Phenomena↗