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Biomedical subjects

B R Brooks

Publications and source records attributed to B R Brooks.

At least 91 records · Page 5Linked to original sources
PubMed1989

The effects of truncating long-range forces on protein dynamics.

This paper considers the effects of truncating long-range forces on protein dynamics. Six methods of truncation that we investigate as a function of cutoff criterion of the long-range potentials are (1) a shifted potential; (2) a switching function; (3) simple atom-atom truncation based on distance; (4) simple atom-atom truncation based on a list which is updated periodically (every 25 steps); (5) simple group-group truncation based on distance; and (6) simple group-group truncation based on a list which is updated periodically (every 25 steps). Based on 70 calculations of carboxymyoglobin we show that the method and distance of long range cutoff have a dramatic effect on overall protein behavior. Evaluation of the different methods is based on comparison of a simulation's rms fluctuation about the average coordinates, the rms deviation from the average coordinates of a no cutoff simulation and from the X-ray structure of the protein. The simulations in which long-range forces are truncated by a shifted potential shows large rms deviations for cutoff criteria less than 14 A, and reasonable deviations and fluctuations at this cutoff distance or larger. Simulations using a switching function are investigated by varying the range over which electrostatic interactions are switched off. Results using a short switching function that switches off the potential over a short range of distances are poor for all cutoff distances. A switching function over a 5-9 A range gives reasonable results for a distance-dependent dielectric, but not using a constant dielectric. Both the atom-atom and group-group truncation methods based on distance shows large rms deviation and fluctuation for short cutoff distances, while for cutoff distances of 11 A or greater, reasonable results are achieved. Although comparison of these to distance-based truncation methods show surprisingly larger rms deviations for the group-group truncation, contrary to simulation studies of aqueous ionic solutions. The results of atom-atom or group-group list-based simulations generally appear to be less stable than the distance-based simulations, and require more frequent velocity scaling or stronger coupling to a heat bath.

Algorithms↗
PubMed1989

Theoretically determined three-dimensional structures for amphipathic segments of the HIV-1 gp41 envelope protein.

Three-dimensional computer models for two segments of the C terminus of gp41, the transmembrane AIDS envelope protein, which may form amphipathic alpha-helices, have been generated using structure prediction techniques combined with energy minimization and molecular dynamics simulations. Regions gp41(772-790) and gp41(828-848) of the HXB2 strain of HIV-1 display extraordinarily high hydrophobic moment maxima as alpha-helices and when in an antiparallel conformation exhibit charge complementarity, implying that they may bind with each other and associate with the membrane. The feasibility of this hypothesis was tested in a series of computer simulations of these peptides, extended by several residues to include additional charge pairing. Beginning with a trial structure in the form of antiparallel alpha-helices of segments 770-794 and 824-856, systematic axial rotations and displacements were used to generate alternative initial states. Molecular dynamics simulations with alpha-helical torsional restraints yielded several approximately cylindrical dimeric structures highly stabilized by numerous salt links and other hydrogen bonds. This suggests that these two regions may fold back on each other in antiparallel fashion to form a loop in the tertiary structure over residues 770-856, with the loop closed by membrane-associated amphipathic alpha-helices with charged sides facing each other. We speculate that such structures could aggregate to form channels or otherwise destabilize the membrane, thereby contributing to the cytopathic effects of the gp120-gp41 complex.

Amino Acid Sequence↗
PubMed1989

Linkage analysis in familial amyotrophic lateral sclerosis.

Familial amyotrophic lateral sclerosis (FALS) constitutes 5 to 10% of cases of ALS and, in most families, its inheritance is consistent with an autosomal dominant trait with age-dependent penetrance. The biochemical abnormality underlying the disorder is unknown. We analyzed DNA from 131 members of 6 multigenerational ALS families, which included 13 affected members, for genetic linkage to 39 expressed and DNA markers, using the techniques of 2-point linkage analysis, multilocus linkage analysis, and exclusion mapping. We identified FALS families with structures suitable for linkage, by computer simulation techniques. A DNA bank established to provide optimum use of available FALS families provided DNA from immortalized lymphoblast cell lines and frozen postmortem tissue. We could not link FALS to any of the markers studied, but excluded chromosome regions unlikely to be a locus of the FALS gene. With the help of this exclusion data, we will concentrate on regions of the human genome that remain unexcluded.

Amyotrophic Lateral Sclerosis↗
PubMed1989

A summary of the current position of TRH in ALS therapy.

The critical points that must be addressed in evaluating ergotropic drugs are exemplified by the current morass of positive and negative results that have been obtained in clinical investigations of TRH or its analogues. Appropriate subject selection is crucial. These patients may have bulbar symptoms, and those features of ALS should be specifically assayed for treatment effects relative to placebo. Gender-specific effects of TRH need to be accounted for in study design. In addition, electrophysiological techniques such as single fiber density may help determine the responsiveness of patients to TRH or its analogues. The clinical significance of an increase in fiber density following TRH or other drugs should be determined, as it will provide insight into the state of motor neurons in the spinal cord of patients with ALS and possibly could be important in determining those who may respond to TRH if such a response is possible. Clinical studies have quite clearly shown conflicting results. Basic studies, however, have shown that response to TRH is state dependent, that is, whether the patient is male or female. Clinical studies have shown that response to TRH is state dependent, that is, it depends on whether the patient has bulbar or nonbulbar signs and is male or female. Future studies must take into consideration this state dependence as a specific feature of the pharmacological action of TRH and its analogues.

Amyotrophic Lateral Sclerosis↗
PubMed1988

Thyrotropin releasing hormone uptake into serum and cerebrospinal fluid following intravenous or subcutaneous administration.

Intravenous thyrotropin releasing hormone (TRH) was administered to 6 amyotrophic lateral sclerosis (ALS) patients at the dose rate of 10 mg/kg. Blood samples were obtained prior to and at 10, 20, 40, 60, and 120 min during the TRH infusions. Lumbar punctures were performed at 90 min following the start of infusion. The mean serum TRH concentration rose from 0.03 +/- 0.02 (SD) to 17 +/- 2 ng/ml by 60 min and remained constant to 120 min. The mean CSF TRH concentration rose 10-fold from 0.02 +/- 0.01 to 0.2 +/- 0.02 ng/ml at 90 min and increased further to 0.5 +/- 0.2 ng/ml at 120 min. Subcutaneous TRH was administered to 4 ALS patients at 2.5 mg/kg and to 5 ALS patients at 5.0 mg/kg. The mean serum TRH concentration increased to 1.4 +/- 0.6 ng/ml (2.5 mg/kg) and 3.2 +/- 1.1 ng/ml (5.0 mg/kg) by 60 min. The mean CSF TRH concentration at 60 min increased to 0.3 +/- 0.08 ng/ml following 2.5 mg/kg TRH and 0.8 +/- 0.04 ng/ml following 5.0 mg/kg TRH. TRH entry into the CSF is comparable following subcutaneous or intravenous administration.

Adult↗
PubMed1988

Delayed immune response in chorea-amyotrophy with spherocytosis.

Progressive CSF lymphocytic pleocytosis and intrathecal IgG-synthesis occurred late in familial amyotrophy, neuropathy, chorea, and dementia with spherocytosis. Immunoblotting showed a serum and CSF antibody apparently directed against glial fibrillary acidic protein. A secondary autoimmune response was probably triggered during the evolution of the neurodegenerative process.

Chorea↗
PubMed1988

Hypoglossal, trigeminal, and facial motoneuron involvement in amyotrophic lateral sclerosis.

Facial, trigeminal, and hypoglossal motoneuron involvement was quantified in 25 amyotrophic lateral sclerosis patients and in normal controls. Measures included (1) maximum voluntary contraction of the lower lip, mandible, and tongue using custom-designed force transducers, (2) clinical functions of each muscle group, and in some patients (3) orofacial mobility using videofluoroscopy. All measures indicated that the tongue muscles were most severely affected, even in patients who initially had symptoms in the extremities.

Adult↗
PubMed1988

Acute posterior multifocal placoid pigment epitheliopathy associated with cerebral vasculitis.

Acute multifocal posterior placoid pigment epitheliopathy (APMPPE) is an unusual self-limited retinal disorder that has been associated with various systemic complications. To our knowledge, three prior cases associated with cerebral vasculitis have been described. This article describes a patient with APMPPE and angiographically documented cerebral vasculitis who was notable because of (a) the presence of two different cerebral ischemic events, occurring 1 month apart, and (b) the long latency (3 months) between the onset of ocular symptoms and the second cerebral ischemic event. Recognition of the association between APMPPE and cerebral vasculitis may permit early treatment of CNS involvement and prevention of morbidity.

Adult↗
PubMed1988

Dosimeters of human exposure to carcinogens: polycyclic aromatic hydrocarbon-macromolecular adducts.

The metabolic activation of polycyclic aromatic hydrocarbons (PAH), for example benzo[a]pyrene, leads to the formation of carcinogen-macromolecular adducts. Methods that make it possible to detect low levels of these adducts in human peripheral blood samples should be useful in the dosimetry of human exposure to carcinogens. We demonstrated previously the usefulness of enzyme immunoassays and of synchronous fluorescence spectroscopy (SFS) for detecting and characterizing low levels of PAH-macromolecular adducts present in synthetic adduct mixtures. These methods have now been refined and applied to the analysis of samples of peripheral blood collected from occupationally exposed individuals (coke-oven workers) and from people attending smoking cessation clinics. The results of both immunoassays and SFS show the presence of benzo[a]pyrene diol epoxide (BPDE)-DNA, BPDE-haemoglobin and other putative PAH-macromolecular adducts in peripheral blood samples from certain individuals.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1987

Absorption mode two-dimensional NOE spectroscopy of exchangeable protons in oligonucleotides.

A new NMR method is described for the generation of absorption mode two-dimensional NOE spectra of oligonucleotides in H2O solution. The method yields spectra that are free of baseline distortions with excellent suppression of the intense H2O resonance. The method is demonstrated for a sample of the dodecamer d(CGCGAATTCGCG)2. All exchangeable base protons are identified and a number of new types of NOE connectivities are observed.

Amines↗
PubMed1987

A three-dimensional model of an anti-lysozyme antibody.

The primary amino acid structure of the lysozyme-binding antibody, HyHEL-10, as determined by amino acid and nucleotide sequencing was utilized to construct a scale model of the Fv (variable region domain of immunoglobulin) using energy-minimized torsional angles of the McPC603 Fv as a prototype template. This model was in turn used as a template for generating a computer-built set of co-ordinates, which were subjected to a total of 600 steps of Adopted Basis Newton-Raphson energy minimizations using the program CHARMM. Only minimal shifts of the backbone (root-mean-square 0.76 A) were required to give an energetically stable structure with a favorable van der Waals' energy. Several notable features were evident from both the scale model and the energy-minimized computer model: (1) the shape of the antibody combining region is that of a very shallow concavity approximately 20 A X 25 A; (2) the concavity is acidic and non-hydrophobic and is bordered by hydrophobic segments; (3) the lower portion of the combining site is dominated by a cluster of tyrosine residues over the L3 and H2 areas; (4) a somatic mutation encoded by the J region of the heavy chain (JH) may contribute significantly to the complementarity of heavy chain H3 to the epitope on hen egg white lysozyme. In addition, the space-filling energy-minimized model revealed that residue 49L, a framework residue, was prominently exposed and accessible in the center of the combining-site concavity. The model suggests that variation in length of complementarity-determining regions may function not only to change directly the shape of the antibody combining site, but may also influence indirectly the nature of the antibody surface by changing the accessibility of residues not usually involved in antigen binding.

Amino Acid Sequence↗
PubMed1987

Theoretically determined three-dimensional structure for the repeating tetrapeptide unit of the circumsporozoite coat protein of the malaria parasite Plasmodium falciparum.

A model for the three-dimensional structure of the repeating Asn-Pro-Asn-Ala tetrapeptide of the immunodominant circumsporozoite protein of Plasmodium falciparum has been developed. A trial structure in the form of a type I beta turn with asparagine side chains hydrogen-bonded to the backbone peptide linkages was used as a starting point. A repeating oligomer of this trial structure was modeled using energy minimization and molecular dynamics computer simulations in conjunction with image boundary conditions. The most stable structure generated is a right-handed 12(38) helix, which is unlike any previously identified protein secondary structure. The helix has 12 residues per turn, corresponding to an angle of twist of 120 degrees per tetrapeptide unit, and a pitch of 4.95 A, corresponding to a rise of 1.65 A per tetrapeptide unit. It is highly stabilized by extensive hydrogen bonding, with each tetrapeptide unit acting as an acceptor for five hydrogen bonds and as a donor for five hydrogen bonds to residues in adjacent turns as well as having four weak internal hydrogen bonds. A number of nearly isoenergetic variations on the most stable structure that still retained the basic 12(38) helical motif were also discovered. The implications of these structures for vaccine development are discussed.

Animals↗
PubMed1987

Physiologic and metabolic response to progressive and prolonged exercise in amyotrophic lateral sclerosis.

Physical work capacity in 35 ALS patients and 6 untrained controls was evaluated during progressive bicycle ergometry. In the ALS patients, maximum oxygen consumption (VO2max) and work capacity (Wmax) drop in relation to the decrease in ALS functional score. However, the oxygen cost (ml O2/kpm) of submaximal exercise was significantly increased. Prolonged submaximal exercise tests in six ALS patients and six matched untrained controls indicated that the exercise-induced increase in plasma free fatty acids, beta-hydroxybutyrate, esterified carnitine, and muscle esterified carnitine was significantly retarded in ALS patients.

3-Hydroxybutyric Acid↗
PubMed1987

Isokinetic assessment in ALS.

Three measures of lower extremity function were compared in a homogenous population of ALS patients. Isokinetic dynamometry was shown to be a sensitive tool for change in strength over time. It demonstrated positive correlations with gait velocity as well as other behavioral measures. Manual muscle tests were relatively insensitive and no more reliable than isokinetics. Isokinetics are a useful adjunct in the assessment of ALS.

Equipment Design↗
PubMed1987

Role of muscular exercise in amyotrophic lateral sclerosis.

The general, systemic, and specific neuromuscular adaptation to physical exercise and training in healthy individuals is reviewed with application to individuals with neuromuscular disease in general and ALS in particular. A pilot study utilizing patients with ALS suggests the cardiopulmonary response to acute exercise is similar to normal individuals. However, a case study of a training response suggests the success of neuromuscular adaptation will be dependent upon the degree of motor neuron involvement.

Adult↗
PubMed1987

Intravenous thyrotropin releasing hormone in amyotrophic lateral sclerosis: autonomic effects.

Heart rate, respiratory rate, systolic and diastolic blood pressure, and oral and skin temperature changes following intravenous administration of TRH occur at lower infusion rates in patients with ALS and bulbar involvement than in patients with ALS without bulbar involvement. This autonomic sensitivity to TRH infusion is characteristic of a more advanced stage of ALS with difficulties in speaking and swallowing. Patients who will be receiving neuropeptides, such as TRH, must be carefully studied to determine whether subclinical bulbar involvement is present. Such patients may require a lower initial dose or dose rate adjustment as well as continual monitoring during neuropeptide administration.

Adult↗
PubMed1987

Intravenous thyrotropin-releasing hormone in patients with amyotrophic lateral sclerosis. Dose-response and randomized concurrent placebo-controlled pilot studies.

Focal, small-to-moderate and transient improvement occurred in the muscle strength and function of patients with ALS who received TRH in dose-response and screening studies. In a small pilot study of 12 patients, 3 months administration of TRH at 10 mg per kg on alternate days resulted in localized increased strength of jaw muscles as well as significant improvement in lower extremity function. Aerobic exercise capacity was particularly improved in patients with ALS following administration of TRH. Autonomic effects of TRH on heart rate, respiration, and blood pressure were not serious and attenuated slightly over the course of the study.

Amyotrophic Lateral Sclerosis↗