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Charles L Webber

Publications and source records attributed to Charles L Webber.

9 recordsLinked to original sources
PubMed2007

A topologically related singularity suggests a maximum preferred size for protein domains.

A variety of protein physicochemical as well as topological properties, demonstrate a scaling behavior relative to chain length. Many of the scalings can be modeled as a power law which is qualitatively similar across the examples. In this article, we suggest a rational explanation to these observations on the basis of both protein connectivity and hydrophobic constraints of residues compactness relative to surface volume. Unexpectedly, in an examination of these relationships, a singularity was shown to exist near 255-270 residues length, and may be associated with an upper limit for domain size. Evaluation of related G-factor data points to a wide range of conformational plasticity near this point. In addition to its theoretical importance, we show by an application of CASP experimental and predicted structures, that the scaling is a practical filter for protein structure prediction.

Binding Sites↗
PubMed2006

Detection of cardiac variability in the isolated rat heart.

Cardiac variability can be assessed from two perspectives: beat-to-beat performance and continuous performance during the cardiac cycle. Linear analysis techniques assess cardiac variability by measuring the physical attributes of a signal, whereas nonlinear techniques evaluate signal dynamics. This study sought to determine if recurrence quantification analysis (RQA), a nonlinear technique, could detect pharmacologically induced autonomic changes in the continuous left ventricular pressure (LVP) and electrographic (EC) signals from an isolated rat heart-a model that theoretically contains no inherent variability. LVP and EC signal data were acquired simultaneously during Langendorff perfusion of isolated rat hearts before and after the addition of acetylcholine (n = 11), norepinephrine (n = 12), or no drug (n = 12). Two-minute segments of the continuous LVP and EC signal data were analyzed by RQA. Findings showed that%recurrence,%determinism, entropy, maxline, and trend from the continuous LVP signal significantly increased in the presence of both acetylcholine and norepinephrine, although systolic LVP significantly increased only with norepinephrine. In the continuous EC signal, the RQA trend variable significantly increased in the presence of norepinephrine. These results suggest that when either the sympathetic or parasympathetic division of the autonomic nervous system overwhelms the other, the dynamics underlying cardiac variability become stationary. This study also shows that information concerning inherent variability in the isolated rat heart can be gained via RQA of the continuous cardiac signal. Although speculative, RQA may be a tool for detecting alterations in cardiac variability and evaluating signal dynamics as a nonlinear indicator of cardiac pathology.

Acetylcholine↗
PubMed2004

EMG recurrence quantifications in dynamic exercise.

This study was designed to evaluate the suitability of nonlinear recurrence quantification analysis (RQA) in assessing electromyograph (EMG) signals during dynamic exercise. RQA has been proven to be effective in analyzing nonstationary signals. The subject group consisted of 19 male patients diagnosed with low back pain. EMG signals were recorded from left and right paraspinal muscles during isoinertial exercise both before and after 12 weeks of regimented physical therapy. Autorecurrence analysis was performed between the left and right EMG signals individually, and cross-recurrence analysis was performed on the left-right EMG pairs. Spectral analysis of the EMG signals was employed as an independent, objective measure of fatigue. Increase in the RQA variable % determinism during the 90-s dynamic tests was found to be a good marker for fatigue. Before physical therapy, this nonlinear marker revealed simultaneous increases in motor unit recruitment within each pool and between left and right pools. After physical therapy, the motor unit recruitment was less within and between pools, indicative of increased fatigue resistance. Finally, fatigue resistance (less increase in % determinism) correlated well with subjective scores of pain relief. Taken together, these latter results indicate that recurrence analysis may be useful in charting the efficacy of a specific exercise therapy program in reducing low back pain by elevating the fatigue threshold.

Electromyography↗
PubMed2003

Protein aggregation/folding: the role of deterministic singularities of sequence hydrophobicity as determined by nonlinear signal analysis of acylphosphatase and Abeta(1-40).

The problem of protein folding vs. aggregation was investigated in acylphosphatase and the amyloid protein Abeta(1-40) by means of nonlinear signal analysis of their chain hydrophobicity. Numerical descriptors of recurrence patterns provided the basis for statistical evaluation of folding/aggregation distinctive features. Static and dynamic approaches were used to elucidate conditions coincident with folding vs. aggregation using comparisons with known protein secondary structure classifications, site-directed mutagenesis studies of acylphosphatase, and molecular dynamics simulations of amyloid protein, Abeta(1-40). The results suggest that a feature derived from principal component space characterized by the smoothness of singular, deterministic hydrophobicity patches plays a significant role in the conditions governing protein aggregation.

Acid Anhydride Hydrolases↗
PubMed2002

Recurrence quantification analysis as a tool for nonlinear exploration of nonstationary cardiac signals.

The complexity, nonlinearity and nonstationarity of the cardiovascular system typically defy comprehensive and deterministic mathematical modeling, except from a statistical perspective. Living systems are governed by numerous, continuously changing, interacting variables in the presence of noise. Cardiovascular signals can be shown to be discontinuous alternations between deterministic trajectories and stochastic pauses (terminal dynamics). One promising approach for assessing such nondeterministic complexity is recurrence quantification analysis (RQA). As reviewed in this paper, strategies implementing quantification of recurrences have been successful in diagnosing changes in nonstationary cardiac signals not easily detected by traditional methods. It is concluded that recurrence quantification analysis is a powerful discriminatory tool which, when properly applied to cardiac signals, can provide objectivity regarding the degree of determinism characterizing the system, state changes, as well as degrees of complexity and/or randomness.

Algorithms↗
PubMed2002

Review of nonlinear analysis of proteins through recurrence quantification.

This review considers the use of a nonlinear signal analysis tool, recurrence quantification analysis, as a method to study sequence/structure relationships of proteins. Four broad categories are discussed: (1) a point of view involving information contained in deterministic aspects of hydrophobicity; (2) the analysis of protein hydrophobicity "singularities"; (3) time-series analysis of protein dynamics simulations; and (4) prediction of protein secondary structure.

Algorithms↗
PubMedDate not supplied

Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins: a computational approach.

The presence of partially folded intermediates along the folding funnel of proteins has been suggested to be a signature of potentially aggregating systems. Many studies have concluded that metastable, highly flexible intermediates are the basic elements of the aggregation process. In a previous paper, we demonstrated how the choice between aggregation and folding behavior was influenced by hydrophobicity distribution patterning along the sequence, as quantified by recurrence quantification analysis (RQA) of the Myiazawa-Jernigan coded primary structures. In the present paper, we tried to unify the "partially folded intermediate" and "hydrophobicity/charge" models of protein aggregation verifying the ability of an empirical relation, developed for rationalizing the effect of different mutations on aggregation propensity of acyl-phosphatase and based on the combination of hydrophobicity RQA and charge descriptors, to discriminate in a statistically significant way two different protein populations: (a) proteins that fold by a process passing by partially folded intermediates and (b) proteins that do not present partially folded intermediates.

Acid Anhydride Hydrolases↗