The number of different types of proteins in the human body approaches 100 000. Proteins are engaged in promoting or controlling virtually every event on which our lives depend. In recent years we have become familiar with the intricate and elegant forms that these molecules adopt in their functional native states. Moreover, we have begun to learn a great deal about the manner in which these structures are attained through the complex process of protein folding, whether this takes place in the laboratory or within the natural environment of the living cell. It is also becoming increasingly evident that biological systems have evolved elaborate procedures to ensure that proteins fold correctly or, if they do not, that they are detected and degraded before any serious harm can ensue to the host organism. Despite these controls, a range of debilitating human diseases is associated with protein misfolding events that result in the malfunctioning of the cellular machinery. Cystic fibrosis is one example where mutations in the gene encoding a crucial transport protein result in the protein folding incorrectly and hence not being secreted in the quantity required for proper function. Other diseases, including some types of familial emphysema, result from mutations that result in improper trafficking of proteins to the sites where they are needed. Recently, however, most attention has been focused on a group of diseases where proteins or fragments of proteins convert from their normally soluble forms to insoluble fibrils or plaques, which accumulate in a variety of organs including the liver, spleen and brain (Fig. 1). The final forms of these aggregates often have a well-defined fibrillar nature, and are known as amyloid (see Box 1), hence the use of the term amyloidosis to describe many of the clinical conditions with which they are associated.
The idea of one gene - one protein - one function has become too simple because increasing numbers of proteins are found to have two or more different functions. The multiple functions of such moonlighting proteins add another dimension to cellular complexity and benefit cells in several ways. However, cells have had to develop sophisticated mechanisms for switching between the distinct functions of these proteins.
The folding reactions of some small proteins show clear evidence of a hierarchic process, whereas others, lacking detectable intermediates, do not. Nevertheless, we argue that both classes fold hierarchically and that folding begins locally. If this is the case, then the secondary structure of a protein is determined largely by local sequence information. Experimental data and theoretical considerations support this argument. Part I of this article reviews the relationship between secondary structures in proteins and their counterparts in peptides.
The Ca2+-calmodulin-dependent protein kinase (CaM kinase) cascade includes three kinases: CaM-kinase kinase (CaMKK); and the CaM kinases CaMKI and CaMKIV, which are phosphorylated and activated by CaMKK. Members of this cascade respond to elevation of intracellular Ca2+ levels and are particularly abundant in brain and in T cells. CaMKK and CaMKIV localize both to the nucleus and to the cytoplasm, whereas CaMKI is only cytosolic. Nuclear CaMKIV regulates transcription through phosphorylation of several transcription factors, including CREB. In the cytoplasm, there is extensive cross-talk between CaMKK, CaMKIV and other signaling cascades, including those that involve the cAMP-dependent kinase (PKA), MAP kinases and protein kinase B (PKB; also known as Akt). Activation of PKB by CaMKK appears to be important in protection of neurons from programmed cell death during development.
The folding reactions of some small proteins show clear evidence of a hierarchic process, whereas others, lacking detectable intermediates, do not. Evidence from folding intermediates and transition states suggests that folding begins locally, and that the formation of native secondary structure precedes the formation of tertiary interactions, not the reverse. Some notable examples in the literature have been interpreted to the contrary. For these examples, we have simulated the local structures that form when folding begins by using the LINUS program with nonlocal interactions turned off. Our results support a hierarchic model of protein folding.
Recent progress in research into programmed cell death has resulted in the identification of the principal protein domains involved in this process. The evolution of many of these domains can be traced back in evolution to unicellular eukaryotes or even bacteria, where the domains appear to be involved in other regulatory functions, Cell-death systems in animals and plants share several conserved domains, in particular the family of apoptotic ATPases; this allows us to suggest a plausible, even if still incomplete, scenario for the evolution of apoptosis,
DNA chips are glass surfaces that represent thousands of DNA fragments arrayed at discrete sites. Hybridization of RNA or DNA-derived samples to DNA chips allows us to monitor expression of mRNAs or the occurrence of polymorphisms in genomic DNA. The technology holds great promise for identifying gene polymorphisms that predispose man to disease, gene regulation events involved in disease progression, and more-effective disease treatments.
Thirty years after Margulis revived the endosymbiosis theory for the origin of mitochondria and chloroplasts, two novel symbiosis hypotheses for the origin of eukaryotes have been put forward. Both propose that eukaryotes arose through metabolic symbiosis (syntrophy) between eubacteria and methanogenic Archaea. They also propose that this was mediated by interspecies hydrogen transfer and that, initially, mitochondria:were anaerobic. These hypotheses explain the mosaic character of eukaryotes (i.e. an archaeal-like genetic machinery and a eubacterial-like metabolism),as well as distinct eukaryotic characteristics (which are proposed to be products of symbiosis). Combined data from comparative genomics, microbial ecology and the fossil record should help to test their validity.
Very simple biochemical systems regulated at the level of gene expression or protein function are capable of complex dynamic behaviour, Among the various patterns of regulation associated with non-linear kinetics, multistability, which corresponds to a true switch between alternate steady states, allows a graded signal to be turned into a discontinuous evolution of the system along several possible distinct pathways, which can be either reversible or irreversible, Multistability plays a significant role in some of the basic processes of life. It might account for maintenance of phenotypic differences in the absence of genetic or environmental differences, as has been demonstrated experimentally for the regulation of the lactose operon in Escherichia coli. Cell differentiation might also be explained as multistability.
Many proteins that were originally characterized on the basis of non-mitochondrial functions have unexpectedly been shown to be identical to mitochondrial-matrix proteins. Most of these proteins are encoded by single nuclear genes and are initially targeted to the mitochondrial matrix. We suggest that mitochondria, as organelles of bacterial origin, possess specific mechanisms for export of proteins to other compartments.
Ascorbate is an essential enzyme cofactor but is often also regarded as an important antioxidant in vivo, protecting against cancer by scavenging DNA-damaging reactive oxygen species. Recent studies suggest that ascorbate some times increases DNA damage in humans. Although there is no evidence that any of these effects are deleterious to humans, we might need to change our thinking about the mechanisms of the antioxidant action of ascorbate in vivo.
The G-protein-signaling pathway is one of the most important signaling cascades used to relay extracellular signals and sensory stimuli to eukaryotic cells. Classically, this signaling system is composed of three major components: G-protein-coupled receptors, heterotrimeric G proteins and effectors. Recently, a new family of proteins, the regulator of G-protein-signaling (RGS) family was discovered, members of which serve as key regulators in this system. RGS proteins function primarily as GTPase-activating proteins (GAPs) for heterotrimeric G-protein alpha (G sub( alpha )) subunits, accelerating the inactivation rate of GTP-bound G sub( alpha ) subunits. Recent experimental data suggest that RGS proteins are involved in regulation of a variety of cellular functions modulated by G-protein signaling, including cell proliferation, cell differentiation, membrane trafficking, cell migration and embryonic development.