Networks of Interactions

Erom a given structure, the NOE effect can be calculated more realistically by complete relaxation matrix analysis. Instead of considering only the distance between two protons, the complete network of interactions is considered (Eig. 8). Approximately, the... 

Moreover, as a consequence of their transient character, a hierarchy of clusters in dynamic equilibrium that may differ in shape and size can be hypothesized [253], Mass, momentum, and charge transport within a cluster of reversed micelles is expected to be strongly enhanced as compared to that among isolated reversed micelles. It has been shown that the dynamics of a network of interacting reversed micelles is successfully described by a model developed by Cates [35,69,254],... 

Kinter A, Arthos J, Cicala C, Fauci AS. Chemokines, cytokines and HIV a complex network of interactions that influence HIV pathogenesis. Immunol Rev 2000 177 88-98. 

Fantuzzi L, Belardelli F, Gessani S. Monocyte/macrophage-derived CC chemokines and their modulation by HIV-1 and cytokines a complex network of interactions influencing viral replication and AIDS pathogenesis. J Leukoc Biol 2003 74(5) 719-725. 

Cellular activities are mediated by complex networks of interactions in response to physiological signals, and the nature of the response is dependent on the cell type and states. These aspects cannot be accounted for by investigating at the genomic or transcriptomic levels alone, as genomes and transcriptomes are fairly conserved between cell states and types within a system. 

There is also considered to be a population of T suppressor cells which acts to down-regulate both T helper cells and B cells, whether through antigen-specific or idiotype-specific mechanisms. The epitopes on the lymphocyte receptor (id-iotype) recognized by the receptor on another lymphocyte (anti-idotype) can form a network of interactions through which suppression may be mediated. 

The experimental exploration and confirmation of protein functions are relatively slow processes and always require dedicated experiments. The analysis of protein-protein associations as such improved remarkably in quality and speed. This is accompanied by the creation of new databases that will reflect the network of interacting proteins (the Protein Function and Metabolic Pathway project, http //bioinformer.ebi. ac.uk 80/newsletter/archives/4/pfmp.html, and the Biomolecular Interaction Network Database project http //bioinfo.mshri.on.ca/ BIND/). These activities contribute to the idea that cellular mechanisms can be better understood when they are seen as a multicomponent networked process. 

Protein function can be described on three levels. Phenotypic function describes the effects of a protein on the entire organism. For example, the loss of the protein may lead to slower growth of the organism, an altered development pattern, or even death. Cellular function is a description of the network of interactions engaged in by a protein at the cellular level. Interactions with other proteins in the cell can help define the lands of metabolic processes in which the protein participates. Finally, molecular function refers to the precise biochemical activity of a protein, including details such as the reactions an enzyme catalyzes or the ligands a receptor binds. 

The regulatory domains of the various receptors overlap, a property that allows different tissues to respond differently to hormonal stimuli. The result is the network of interactions that makes the body so sensitive and responsive. 

Specifically, in the first step of the energy cascade, the light is captured by the DVB dimer located in the core of the complex. The energy is then transferred to peripherally located bilins (MBV, PCB 158) through a complex network of interactions that, owing to the very similar timescales and spectral features, are hard to separate. Probably, energy migration from DBV bilins to the MBV bilins occurs on a timescale (T) 0.6 ps) faster than the transfer... 

In multicellular organisms, the space between cells is largely occupied by an intricate network of interacting macromolecules that constitute the extracellular matrix. This matrix surrounds, supports and regulates the behavior of the cells, such as fibroblasts, that secrete the extracellular matrix. Together, the matrix with these cells constitutes the connective tissue. 

In contrast to methods involving single substitutions, combinatorial strategies are ideally suited for evaluating the complex network of interactions in proteins that ultimately determine form and function [73]. As shown in the mechanistic and structural investigations of chorismate mutases, degenerate protein ensembles can illuminate subtle trends that might be missed in analyses of individual amino acid replace-... 

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