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1.
This review outlines the use of expressed protein ligation (EPL) to study protein structure, function and stability. EPL is a chemoselective ligation method that allows the selective ligation of unprotected polypeptides from synthetic and recombinant origin for the production of semi-synthetic protein samples of well-defined and homogeneous chemical composition. This method has been extensively used for the site-specific introduction of biophysical probes, unnatural amino acids, and increasingly complex post-translational modifications. Since it was introduced 10 years ago, EPL applications have grown increasingly more sophisticated in order to address even more complex biological questions. In this review, we highlight how this powerful technology combined with standard biochemical analysis techniques has been used to improve our ability to understand protein structure and function. 相似文献
2.
Defining a neuron: neuronal ELAV proteins 总被引:1,自引:1,他引:0
Neuronal cells strongly depend on the control exerted by RNA-binding proteins (RBPs) on gene expression for the establishment
and maintenance of their phenotype. Neuronal ELAV (nELAV) proteins are RBPs able to influence virtually every aspect of the
postsynthesis fate of bound mRNAs, from polyadenylation, alternative splicing and nuclear export to cytoplasmic localization,
stability and translation. They enhance gene expression through the last two, best documented activities, increasing mRNA
half-life and promoting protein synthesis by a still-unknown molecular mechanism. Developmentally, nELAV proteins have been
shown to act as inducers of the transition between neural stem/progenitor cells and differentiation-committed cells, also
assisting these neuroblasts in the completion of their maturation program. In brain physiology, they are also the first RBPs
demonstrated to have a pivotal role in memory, where they probably control mRNA availability for translation in subcellular
domains, thereby providing a biochemical means for selective increase in synaptic strength.
Received 15 January 2007; received after revision 10 August 2007; accepted 6 September 2007 相似文献
3.
Type-2 Cu sites are found in all the major branches of life and are often involved in the catalysis of oxygen species. Four
type-2 Cu protein families are selected as model systems for review: amine oxidases, Cu monooxygenases, nitrite reductase/multicopper
oxidase, and CuZn superoxide dismutase. For each model protein, the availability of multiple crystal structures and detailed
enzymological studies provides a detailed molecular view of the type-2 Cu site and delineation of the mechanistic role of
the Cu in biological function. Comparison of these model proteins leads to the identification of common properties of the
Cu sites and insight into the evolution of the trinuclear active site found in multicopper oxidases.
Received 6 July 2007; accepted 18 July 2007 相似文献
4.
Retinal proteins function as photoreceptors and ion pumps. Xanthorhodopsin of Salinibacter ruber is a recent addition to this diverse family. Its novel and distinctive feature is a second chromophore, a carotenoid, which
serves as light-harvesting antenna. Here we discuss the properties of this carotenoid/retinal complex most relevant to its
function (such as the specific binding site controlled by the retinal) and its relationship to other retinal proteins (bacteriorhodopsin,
archaerhodopsin, proteorhodopsin and retinal photoreceptors of archaea and eukaryotes). Antenna addition to a retinal protein
has not been observed among the archaea and emerged in bacteria apparently in response to environmental conditions where light-harvesting
becomes a limiting factor in retinal protein functioning.
Received 2 April 2007; received after revision 14 May 2007; accepted 16 May 2007 相似文献
5.
Jensen MR Hass MA Hansen DF Led JJ 《Cellular and molecular life sciences : CMLS》2007,64(9):1085-1104
Metal ions play a key role for the function of many proteins. The interaction of the metal ion with the protein and its involvement
in the function of the protein vary widely. In some proteins, the metal ion is bound tightly to the ligand residues and may
be the key player in the function of the protein, as in the case of blue copper proteins. In other proteins, the metal ion
is bound only temporarily and loosely to the protein, as in the case of some metalloenzymes and other proteins where the metal
ion acts as a cofactor necessary for the function of the protein. Such proteins are often known as metal ion-activated proteins.
The review focuses on recent nuclear magnetic resonance (NMR) studies of a series of metal-dependent proteins and the characterization
of the metal-binding sites. In particular, we focus on NMR techniques for studying metal binding to proteins such as chemical
shift mapping, paramagnetic NMR and changes in backbone dynamics upon metal binding.
Received 12 October 2006; received after revision 30 November 2006; accepted 5 February 2007 相似文献
6.
Coronavirus envelope protein is a small membrane protein and minor component of the virus particles. It plays important roles
in virion assembly and morphogenesis, alteration of the membrane permeability of host cells and virus-host cell interaction.
Here we review recent progress in characterization of the biochemical properties, membrane topology and functions of the protein.
Received 27 February 2007; received after revision 4 April 2007; accepted 26 April 2007 相似文献
7.
Lisowska E 《Cellular and molecular life sciences : CMLS》2002,59(3):445-455
Glycosylation of proteins is a common event and contributes to protein antigenic properties. Most data have been obtained
from model studies on glycoprotens with well-defined structure or synthetic glycopeptides and their respective monoclonal
antibodies. Antibodies raised against glycoprotein antigens may be specific for their carbohydrate units which are recognized
irrespective of the protein carrier (carbohydrate epitopes), or in the context of the adjacent amino acid residues (glycopeptidic
epitopes). Conformation or proper exposure of peptidic epitopes of glycoproteins is also frequently modulated by glycosylation
due to intramolecular carbohydrate-protein interactions. The effects of glycosylation are broad: glycosylation may 'inactivate'
the peptidic epitope or may be required for its reactivity with the antibody, depending on the structure of the antigenic
site and antibody fine specificity. Evidence is increasing that similar effects of glycosylation pertain to T cell-dependent
cellular immune responses. Glycosylated peptides can be bound and presented by MHC class I or II molecules and elicit glycopeptide-specific
T cell clones.
Received 5 July 2001; received after revision 9 October 2001; accepted 11 October 2001 相似文献
8.
Courtois G 《Cellular and molecular life sciences : CMLS》2008,65(7-8):1123-1132
CYLD is a protein with tumor suppressor properties which was originally discovered associated with cylindromatosis, an inherited
cancer exclusively affecting the folicullo-sebaceous-apocrine unit of the epidermis. CYLD exhibits deubiquitinating activity
and acts as a negative regulator of NF-κB and JNK signaling through its interaction with NEMO and TRAF2. Recent data suggest
that this is unlikely to be its unique function in vivo. CYLD has also been shown to control other seemingly disparate cellular processes, such as proximal T cell receptor signaling,
TrkA endocytosis and mitosis. In each case, this enzyme appears to act by regulating a specific type of polyubiquitination,
K63 polyubiquitination, that does not result in recognition and degradation of proteins by the proteasome but instead controls
their activity through diverse mechanisms.
Received 6 October 2007; received after revision 2 November 2007; accepted 23 November 2007 相似文献
9.
γ-Secretase is a promiscuous protease that cleaves bitopic membrane proteins within the lipid bilayer. Elucidating both the
mechanistic basis of γ-secretase proteolysis and the precise factors regulating substrate identification is important because
modulation of this biochemical degradative process can have important consequences in a physiological and pathophysiological
context. Here, we briefly review such information for all major classes of intramembranously cleaving proteases (I-CLiPs),
with an emphasis on γ-secretase, an I-CLiP closely linked to the etiology of Alzheimer’s disease. A large body of emerging
data allows us to survey the substrates of γ-secretase to ascertain the conformational features that predispose a peptide
to cleavage by this enigmatic protease. Because substrate specificity in vivo is closely linked to the relative subcellular compartmentalization of γ-secretase and its substrates, we also survey the
voluminous body of literature concerning the traffic of γ-secretase and its most prominent substrate, the amyloid precursor
protein.
Received 4 October 2007; received after revision 1 December 2007; accepted 7 December 2007 相似文献
10.
Fändrich M 《Cellular and molecular life sciences : CMLS》2007,64(16):2066-2078
Amyloid fibrils occur inside the human body, associated with ageing or a group of diseases that includes, amongst others,
Alzheimer’s disease, atherosclerosis and type II diabetes. Many natural polypeptide chains are able to form amyloid fibrils
in vivo or in vitro, and this ability has been suggested to represent an inherent consequence of the chemical structure of the polypeptide chain.
Recent literature has provided a wealth of information about the structure of aggregates, precipitates, amyloid fibrils and
other types of fibrillar polypeptide assemblies. However, the biophysical meaning associated with these terms can differ considerably
depending on the context of their usage. This overview presents a structural comparison of amyloid fibrils and other types
of polypeptide assemblies and defines amyloid fibrils, based on structural considerations, as fibrillar polypeptide aggregates
with a cross-β conformation.
Received 1 March 2007; received after revision 15 March 2007; accepted 25 April 2007 相似文献
11.
Alternative splicing contributes greatly to proteomic complexity. How it is regulated by external stimuli to sculpt cellular properties, particularly the highly diverse and malleable neuronal properties, is an underdeveloped area of emerging interest. A number of recent studies in neurons and endocrine cells have begun to shed light on its regulation by calcium signals. Some mechanisms include changes in the trans-acting splicing factors by phosphorylation, protein level, alternative pre-mRNA splicing, and nucleocytoplasmic redistribution of proteins to alter protein–RNA or protein–protein interactions, as well as modulation of chromatin states. Importantly, functional analyses of the control of specific exons/splicing factors in the brain point to a crucial role of this regulation in synaptic maturation, maintenance, and transmission. Furthermore, its deregulation has been implicated in the pathogenesis of neurological disorders, particularly epilepsy/seizure. Together, these studies have not only provided mechanistic insights into the regulation of alternative splicing by calcium signaling but also demonstrated its impact on neuron differentiation, function, and disease. This may also help our understanding of similar regulations in other types of cells. 相似文献
12.
Jedrzejas MJ 《Cellular and molecular life sciences : CMLS》2007,64(21):2799-2822
Bacteria present a variety of molecules either on their surface or in a cell-free form. These molecules take part in numerous
processes in the interactions with their host, with its tissues and other molecules. These molecules are essential to bacterial
pathogenesis either during colonization or the spread/invasion stages, and most are virulence factors. This review is focused
on such molecules using Streptococcus pneumoniae, a Gram-positive bacterium, as an example. Selected surface proteins are introduced, their structure described, and, whenever
available, their mechanisms of function on an atomic level are explained. Such mechanisms for hyaluronate lyase, pneumococcal
surface protein A, pneumolysin, histidine-triad and fibronectin-binding proteins are discussed. Elucidation of molecular mechanisms
of virulence factors is essential for the understanding of bacteria and their functional properties. Structural biology appears
pivotal for these studies, as structural and mechanistic insights facilitate rational approach to the development of new treatments.
Received 12 March 2007; received after revision 28 June 2007; accepted 18 July 2007 相似文献
13.
Ulrich Salzer Julius Kostan Kristina Djinović-Carugo 《Cellular and molecular life sciences : CMLS》2017,74(13):2413-2438
The BAR domain is the eponymous domain of the “BAR-domain protein superfamily”, a large and diverse set of mostly multi-domain proteins that play eminent roles at the membrane cytoskeleton interface. BAR domain homodimers are the functional units that peripherally associate with lipid membranes and are involved in membrane sculpting activities. Differences in their intrinsic curvatures and lipid-binding properties account for a large variety in membrane modulating properties. Membrane activities of BAR domains are further modified and regulated by intramolecular or inter-subunit domains, by intermolecular protein interactions, and by posttranslational modifications. Rather than providing detailed cell biological information on single members of this superfamily, this review focuses on biochemical, biophysical, and structural aspects and on recent findings that paradigmatically promote our understanding of processes driven and modulated by BAR domains. 相似文献
14.
Navarro S Aleu J Jiménez M Boix E Cuchillo CM Nogués MV 《Cellular and molecular life sciences : CMLS》2008,65(2):324-337
Human eosinophil cationic protein (ECP)/ ribonuclease 3 (RNase 3) is a protein secreted from the secondary granules of activated
eosinophils. Specific properties of ECP contribute to its cytotoxic activities associated with defense mechanisms. In this
work the ECP cytotoxic activity on eukaryotic cell lines is analyzed. The ECP effects begin with its binding and aggregation
to the cell surface, altering the cell membrane permeability and modifying the cell ionic equilibrium. No internalization
of the protein is observed. These signals induce cell-specific morphological and biochemical changes such as chromatin condensation,
reversion of membrane asymmetry, reactive oxygen species production and activation of caspase-3-like activity and, eventually,
cell death. However, the ribonuclease activity component of ECP is not involved in this process as no RNA degradation is observed.
In summary, the cytotoxic effect of ECP is attained through a mechanism different from that of other cytotoxic RNases and
may be related with the ECP accumulation associated with the inflammatory processes, in which eosinophils are present.
Received 26 October 2007; accepted 23 November 2007 相似文献
15.
Vesicle fusion is a ubiquitous biological process involved in membrane trafficking and a variety of specialised events such
as exocytosis and neurite outgrowth. The energy to drive biological membrane fusion is provided by fusion proteins called
SNAREs. Indeed, SNARE proteins play critical roles in neuronal development as well as neurotransmitter and hormone release.
SNARE proteins form a very tight alpha-helical bundle that can pull two membranes together, thereby initiating fusion. Whereas
a great deal of attention has been paid to partner proteins that can affect SNARE function, recent genetic and biochemical
evidence suggests that local lipid environment may be as important in SNARE regulation. Direct lipid modification of SNARE
fusion proteins and their regulation by fatty acids following phospholipase action will be discussed here in detail. Our analysis
highlights the fact that lipids are not a passive platform in vesicle fusion but intimately regulate SNARE function.
Received 20 December 2006; received after revision 6 February 2007; accepted 15 March 2007 相似文献
16.
In recent years the interest in antimicrobial proteins and peptides and their mode of action has been rapidly increasing due
to their potential to prevent and combat microbial infections in all areas of life. A detailed knowledge about the function
of such proteins is the most important requirement to consider them for future application. Our research in recent years has
been focused on the low molecular weight, cysteine-rich and cationic antifungal protein PAF from Penicillium chrysogenum, which inhibits the growth of opportunistic zoo-pathogens including Aspergillus fumigatus, numerous plant-pathogenic fungi and the model organism Aspergillus nidulans. So far, the experimental results indicate that PAF elicits hyperpolarization of the plasma membrane and the activation of
ion channels, followed by an increase in reactive oxygen species in the cell and the induction of an apoptosis-like phenotype.
Detailed knowledge about the molecular mechanism of action of antifungal proteins such as PAF contributes to the development
of new antimicrobial strategies that are urgently needed.
Received 09 August 2007; received after revision 17 September 2007; accepted 19 September 2007 相似文献
17.
OSBP (oxysterol-binding protein) and ORPs (OSBP-related proteins) constitute an enigmatic eukaryotic protein family that is
united by a signature domain that binds oxysterols, sterols, and possibly other hydrophobic ligands. The human genome contains
12 OSBP/ORP family members genes, while that of the budding yeast Saccharomyces cerevisiae encodes seven OSBP homologues (Osh). Of these, Osh4 (also referred to as Kes1) has been the most widely studied to date.
Recently, three-dimensional crystal structures of Osh4 with and without sterols bound within the core of the protein were
determined. The core consists of 19 anti-parallel β-sheets that form a near-complete β-barrel. Recent work has suggested that
Osh proteins facilitate the non-vesicular transport of sterols in vivo and in vitro, while other evidence supports a role for Osh proteins in the regulation of vesicular transport and lipid metabolism.This
article will review recent advances in the study of ORP/Osh proteins and will discuss future research issues regarding the
ORP/Osh family.
Received 17 July 2007; received after revision 14 August 2007; accepted 12 September 2007 相似文献
18.
The terminase enzyme from bacteriophage lambda: a DNA-packaging machine 总被引:14,自引:0,他引:14
Catalano CE 《Cellular and molecular life sciences : CMLS》2000,57(1):128-148
19.
Molecular adaptations to cold in psychrophilic enzymes 总被引:13,自引:0,他引:13
Feller G 《Cellular and molecular life sciences : CMLS》2003,60(4):648-662
Psychrophiles or cold-loving organisms successfully colonize cold environments of the Earth's biosphere. To cope with the reduction of chemical reaction rates induced by low temperatures, these organisms synthesize enzymes characterized by a high catalytic activity at low temperatures associated, however, with low thermal stability. Thanks to recent advances provided by X-ray crystallography, protein engineering and biophysical studies, we are beginning to understand the molecular adaptations responsible for these properties which appear to be relatively diverse. The emerging picture suggests that psychrophilic enzymes utilize an improved flexibility of the structures involved in the catalytic cycle, whereas other protein regions if not implicated in catalysis may or may not be subjected to genetic drift. 相似文献
20.
sHsps and their role in the chaperone network 总被引:17,自引:0,他引:17
Haslbeck M 《Cellular and molecular life sciences : CMLS》2002,59(10):1649-1657
Small Hsps (sHsps) encompass a widespread but diverse class of proteins. These low molecular mass proteins (15—42 kDa) form
dynamic oligomeric structures ranging from 9 to 50 subunits. sHsps display chaperone function in vitro, and in addition they
have been suggested to be involved in the inhibition of apoptosis, organisation of the cytoskeleton and establishing the refractive
properties of the eye lens in the case of α-crystallin. How these different functions can be explained by a common mechanism
is unclear at present. However, as most of the observed phenomena involve nonnative protein, the repeatedly reported chaperone
properties of sHsps seem to be of key importance for understanding their function. In contrast to other chaperone families,
sHsps bind several nonnative proteins per oligomeric complex, thus representing the most efficient chaperone family in terms
of the quantity of substrate binding. In some cases, the release of substrate proteins from the sHsp complex is achieved in
cooperation with Hsp70 in an ATP-dependent reaction, suggesting that the role of sHsps in the network of chaperones is to
create a reservoir of nonnative refoldable protein. 相似文献