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Protein folding reviews: 2003
(51 References)
Baldwin, R. L. (2003). "In search of the energetic role of peptide hydrogen bonds." J Biol Chem 278(20): 17581-8.
Bannwarth, M. and G. E. Schulz (2003). "The expression of outer membrane proteins for crystallization." Biochim Biophys Acta 1610(1): 37-45.
The production of sufficient amounts of chemically and conformationally homogenous protein is a major requirement for successful crystallization and structure determination. With membrane proteins, this constitutes a particular problem because the membrane volume is limited and the organisms are usually very sensitive to changes in membrane properties brought about by massive protein insertion. Moreover, the extraction of membrane proteins from the membrane with detergents is generally a harsh treatment, which gives rise to conformational aberrations. A number of successful procedures for functional expression followed by purification are reviewed here together with nonfunctional expression into inclusion bodies and subsequent (re)folding to produce functional proteins. Most of the data are for prokaryotic outer membrane proteins, but the outer membrane proteins of eukaryotic organelles are also considered as they do show similar features.
Barboro, P., C. D'Arrigo, et al. (2003). "An intranuclear frame for chromatin compartmentalization and higher-order folding." J Cell Biochem 88(1): 113-20.
Recent ultrastructural, immunoelectron, and confocal microscopy observations done in our laboratory [Barboro et al. [2002] Exp. Cell. Res. 279:202-218] have confirmed that lamins and the nuclear mitotic apparatus protein (NuMA) are localized inside the interphase nucleus in a polymerized form. This provided evidence of the existence of a RNA stabilized lamin/NuMA frame, consisting of a web of thin ( approximately 3 and approximately 5 nm) lamin filaments to which NuMA is anchored mainly in the form of discrete islands, which might correspond to the minilattices described by Harborth et al. [1999] (EMBO. J. 18:1689-1700). In this article we propose that this scaffold is involved in the compartmentalization of both chromatin and functional domains and further determines the higher-order nuclear organization. This hypothesis is strongly supported by the scrutiny of different structural transitions which occur inside the nucleus, such as chromatin displacement and rearrangements, the collapse of the internal nuclear matrix after RNA digestion and the disruption of chromosome territories induced by RNase A and high salt treatment. All of these destructive events directly depend on the loss of the stabilizing effect exerted on the different levels of structural organization by the interaction of RNA with lamins and/or NuMA. Therefore, the integrity of nuclear RNA must be safeguarded as far as possible to isolate the matrix in the native form. This material will allow for the first time the unambiguous ultrastructural localization inside the INM of the components of the functional domains, so opening new avenues of investigation on the mechanisms of gene expression in eukaryotes.
Bartlett, G. J., A. E. Todd, et al. (2003). "Inferring protein function from structure." Methods Biochem Anal 44: 387-407.
Booth, P. J. (2003). "The trials and tribulations of membrane protein folding in vitro." Biochim Biophys Acta 1610(1): 51-6.
Membrane proteins are hard to handle and consequently the purification of functional protein in milligram quantities is a major problem. One reason for this is that once integral membrane proteins are outside their native membrane, they are prone to aggregation, are unstable and are frequently only partially functional. Knowledge of membrane protein folding mechanisms in vitro can help to understand the causes of these problems and work toward strategies to disaggregate and fold proteins correctly. Kinetic and stability studies are emerging on membrane protein folding, mainly on bacterial proteins. Mutagenesis methods have also been used to probe specific structural features or bonds in proteins. In addition, manipulation of lipid properties can be used to improve the efficiency of folding as well as the stability and function of the protein.
Bouvier, M. (2003). "Accessory proteins and the assembly of human class I MHC molecules: a molecular and structural perspective." Mol Immunol 39(12): 697-706.
The cell-surface presentation of antigenic peptides by class I major histocompatibility complex (MHC) molecules to CD8+ T-cell receptors is part of an immune surveillance mechanism aimed at detecting foreign antigens. This process is initiated in the endoplasmic reticulum (ER) with the folding and assembly of class I MHC molecules which are then transported to the cell surface via the secretory pathway. In recent years, several accessory proteins have been identified as key components of the class I maturation process in the ER. These proteins include the lectin chaperones calnexin (CNX) and calreticulin (CRT), the thiol-dependent oxidoreductase ERp57, the transporter associated with antigen processing (TAP), and the protein tapasin. This review presents the most recent advances made in characterizing the biochemical and structural properties of these proteins, and discusses how this knowledge advances our current understanding of the molecular events underlying the folding and assembly of human class I MHC molecules in the ER.
Bruser, T. and C. Sanders (2003). "An alternative model of the twin arginine translocation system." Microbiol Res 158(1): 7-17.
The twin arginine translocation (Tat) system is a machinery which can translocate folded proteins across energy transducing membranes. Currently it is supposed that Tat substrates bind directly to Tat translocon components before a ApH-driven translocation occurs. In this review, an alternative model is presented which proposes that membrane integration could precede Tat-dependent translocation. This idea is mainly supported by the recent observations of Tat-independent membrane insertion of Tat substrates in vivo and in vitro. Membrane insertion may allow i) a quality control of the folded state by membrane bound proteases like FtsH, ii) the recognition of the membrane spanning signal peptide by Tat system components, and iii) a pulling mechanism of translocation. In some cases of folded Tat substrates, the membrane targeting process may require ATP-dependent N-terminal unfolding-steps.
Cookson, M. R. (2003). "Pathways to Parkinsonism." Neuron 37(1): 7-10.
A novel gene for Parkinson's disease (PD), DJ-1, has been identified that encodes a multifunctional product with several known protein-protein interactions and effects on gene expression. Here, I outline how it is possible to construct hypotheses that place DJ-1 in different relationships to the other known PD genes, alpha-synuclein and parkin. The identification of multiple genetic causes will provide further impetus to describe the pathway leading to PD.
Daggett, V. and A. R. Fersht (2003). "Is there a unifying mechanism for protein folding?" Trends Biochem Sci 28(1): 18-25.
Proteins appear to fold by diverse pathways, but variations of a simple mechanism - nucleation-condensation - describe the overall features of folding of most domains. In general, secondary structure is inherently unstable and its stability is enhanced by tertiary interactions. Consequently, an extensive interplay of secondary and tertiary interactions determines the transition-state for folding, which is structurally similar to the native state, being formed in a general collapse (condensation) around a diffuse nucleus. As the propensity for stable secondary structure increases, folding becomes more hierarchical and eventually follows a framework mechanism where the transition state is assembled from pre-formed secondary structural elements.
Driscoll, M. and B. Gerstbrein (2003). "Dying for a cause: invertebrate genetics takes on human neurodegeneration." Nat Rev Genet 4(3): 181-94.
If invertebrate neurons are injured by hostile environments or aberrant proteins they die much like human neurons, indicating that the powerful advantages of invertebrate molecular genetics might be successfully used for testing specific hypotheses about human neurological diseases, for drug discovery and for non-biased screens for suppressors and enhancers of neurodegeneration. Recent molecular dissection of the genetic requirements for hypoxia, excitotoxicity and death in models of Alzheimer disease, polyglutamine-expansion disorders, Parkinson disease and more, is providing mechanistic insights into neurotoxicity and suggesting new therapeutic interventions. An emerging theme is that neuronal crises of distinct origins might converge to disrupt common cellular functions, such as protein folding and turnover.
Ellgaard, L. and A. Helenius (2003). "Quality control in the endoplasmic reticulum." Nat Rev Mol Cell Biol 4(3): 181-91.
The endoplasmic reticulum (ER) has a quality-control system for 'proof-reading' newly synthesized proteins, so that only native conformers reach their final destinations. Non-native conformers and incompletely assembled oligomers are retained, and, if misfolded persistently, they are degraded. As a large fraction of ER-synthesized proteins fail to fold and mature properly, ER quality control is important for the fidelity of cellular functions. Here, we discuss recent progress in understanding the conformation-specific sorting of proteins at the level of ER retention and export.
Feldman, M. F. and G. R. Cornelis (2003). "The multitalented type III chaperones: all you can do with 15 kDa." FEMS Microbiol Lett 219(2): 151-8.
Despite the fact that type III chaperones were discovered approximately 10 years ago, the precise role of most of them is still mysterious. A panoply of functions has been proposed for the members of this family of proteins. Type III chaperones have been suggested to act as anti-aggregation and stabilizing factors. They have also been proposed to keep their substrates in unfolded or partially folded structures, set a hierarchy on secretion, and participate in the regulation of the transcription of the type III substrates. Here, we review this enigmatic family of proteins, and discuss the experimental data supporting the roles proposed for type III chaperones.
Focher, F., S. Spadari, et al. (2003). "Antivirals at the mirror: the lack of stereospecificity of some viral and human enzymes offers novel opportunities in antiviral drug development." Curr Drug Targets Infect Disord 3(1): 41-53.
The enantioselectivity of enzymes, namely the property of enzymes to recognise and metabolise only one of the two enantiomers of chiral molecules, is related to the chiral structure of the enzymes, reflecting the three-dimensional folding of the polypeptide backbone and the orientation of the amino acid side chains in the folded molecule. Because of the chirality of the amino acids (L), the chemistry of life should be highly sensitive to different enantiomers of chiral substrates. However, in a world consisting only of D-nucleosides and L-amino acids, an enzyme which lacks enantio-selectivity does not reduce its fitness, since there is no chance of molecular misunderstanding when no other choice is available. Thus, although enantioselectivity is theoretically essential for life we do not expect to be always present among the biochemical properties of enzymes. If this is the case for key enzymes involved in virus infection or cancer, how to exploit such lack of enantioselectivity for a novel approach to antiviral or anticancer chemotherapy? The present review will discuss the possible lack of enantioselectivity of enzymes and its relevance for the developing of novel drugs with the inverted optical configuration.
Godzik, A. (2003). "Fold recognition methods." Methods Biochem Anal 44: 525-46.
We are still missing a basic understanding of sequence/structure/function relationships in proteins. Analogy-based prediction algorithms remain the only reliable fold prediction tools. New methods, such as threading and hybrid threading/sequence fold recognition, can often recognize even the most distant homologues and, in some cases, even unrelated proteins with similar overall structures. This knowledge pushed the envelope of analogy-based function analysis to the point that the majority of newly sequenced genomes can be tentatively assigned to already characterized protein superfamilies. However, at this evolutionary distance, fold prediction is no longer equivalent to function prediction. Instead of having the same exact function, distantly related proteins might share some functional analogy that is not obvious to the casual observer. The main challenge facing the fold recognition field is to develop tools to follow the structure prediction with function prediction and analysis.
Golbe, L. I. (2003). "Alpha-synuclein and Parkinson's disease." Adv Neurol 91: 165-74.
Gregersen, N., P. Bross, et al. (2003). "[Conformational diseases]." Ugeskr Laeger 165(8): 801-5.
Conformational diseases are diseases where cellular functions are compromised because of misfolded proteins. The conceptional framework of conformational diseases is found in the cellular protein quality control systems which in the normal and young cell eliminate misfolded proteins. Many inherited genetic defects result in the misfolding of proteins, which may lead to recessive disorders if the proteins in question are totally or partly eliminated or to dominant diseases if the proteins slip through the protein quality control and accumulate in the cell. These inherited diseases are all early onset. Misfolding may also occur in proteins with an intrinsic ability to aggregate and in oxidatively damaged proteins, which accumulate by ageing. If the protein quality control systems are not sufficiently efficient cell toxic protein complexes may accumulate. This pathogenesis is a major contributing factor in the development of late onset neurodegenerative disorders.
Hatakeyama, S. and K. I. Nakayama (2003). "U-box proteins as a new family of ubiquitin ligases." Biochem Biophys Res Commun 302(4): 635-45.
Ubiquitin-protein ligases (E3s) determine the substrate specificity of ubiquitylation and, until recently, had been classified into two families, the HECT and RING-finger families. The U-box is a domain of approximately 70 amino acids that is present in proteins from yeast to humans. The prototype U-box protein, yeast Ufd2, was identified as a ubiquitin chain assembly factor (E4) that cooperates with a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and an E3 to catalyze the formation of a ubiquitin chain on artificial substrates. We recently showed that mammalian U-box proteins, in conjunction with an E1 and an E2, mediate polyubiquitylation in the absence of a HECT type or RING-finger type E3. U-box proteins have thus been defined as a third family of E3s. We here review recent progress in the characterization of U-box proteins and of their role in the quality control system that underlies the cellular stress response to the intracellular accumulation of abnormal proteins.
Hetz, C. and C. Soto (2003). "Protein misfolding and disease: the case of prion disorders." Cell Mol Life Sci 60(1): 133-43.
Recent findings strongly support the hypothesis that diverse human disorders, including the most common neurodegenerative diseases, arise from misfolding and aggregation of an underlying protein. Despite the good evidence for the involvement of protein misfolding in disease pathogenesis, the mechanism by which protein conformational changes participate in the disease is still unclear. Among the best-studied diseases of this group are the transmissible spongiform encephalopathies or prion-related disorders, in which misfolding of the normal prion protein plays a key role in the disease. In this article we review recent data on the link between prion protein misfolding and the pathogensis of spongiform encephalopathies.
Hiniker, A. and J. C. Bardwell (2003). "Disulfide bond isomerization in prokaryotes." Biochemistry 42(5): 1179-85.
Hood, D. A., P. J. Adhihetty, et al. (2003). "Mitochondrial biogenesis and the role of the protein import pathway." Med Sci Sports Exerc 35(1): 86-94.
PURPOSE: The importance of the mitochondrial protein import pathway, discussed relative to other steps involved in the overall biogenesis of the organelle, are reviewed. RESULTS: Mitochondrial biogenesis is a product of complex interactions between the nuclear and mitochondrial genomes. Signaling pathways, such as those activated by exercise, initiate the activation of transcription factors that increase the production of mRNA from nuclear and mitochondrial DNA. Nuclear gene products are translated in the cytosol as precursor proteins with inherent targeting signals. These precursor proteins interact with molecular chaperones that direct them to the import machinery of the outer membrane (Tom complex). The precursor is unfolded and transferred through the outer membrane, across the intermembrane space to the mitochondrial inner membrane translocases (Tim complex). Intramitochondrial components (mtHSP70) pull the precursor into the matrix, cleave off the targeting sequence (mitochondrial processing peptidase), and refold the protein (HSP60, cpn10) into its mature conformation. Physiological stressors such as contractile activity and thyroid hormone accelerate protein import into the mitochondria, coincident with an increase in the expression of some components of the import machinery. This is important for the overall expansion of the mitochondrial reticulum. Conversely, impairments in the import process can be a cause of mitochondrial dysfunction and disease. CONCLUSIONS: Efforts to further characterize the components of the import machinery, to define the role of specific machinery components on the import rate, and to examine protein import function in a variety of mitochondrial diseases are warranted.
Hoshino, M. (2003). "[Structural analysis of amyloid-fibrils of beta 2-microglobulin]." Seikagaku 75(2): 143-8.
Ito, H., Y. Inaguma, et al. (2003). "[Small heat shock proteins participate in the regulation of cellular aggregates of misfolded protein]." Nippon Yakurigaku Zasshi 121(1): 27-32.
Molecular chaperones participate in folding of many proteins and several families are known to exist in mammalian cells including the small heat shock protein (sHSP) family. sHSPs have a molecular mass of 15-30 kDa and are known to be induced and phosphorylated in response to various stimuli. There are several reports describing the correlation between sHSPs and degenerative diseases. We have been reported that Hsp27 and alpha B-crystallin were recruited to aggresome when cells were treated with proteasome inhibitors. Expression of Hsp27 suppresses the cell death induced by expression of expanded polyglutamine via down regulation of the oxidative stress pathway. Recently, a missense mutation in alpha B-crystallin, R120G, has been found in a French family suffering from desmin-related myopathy. Moreover, transgenic mice expressing R120G alpha B-crystallin exhibit symptoms similar to desmin-related myopathy. We recently examined the interaction of R120G alpha B-crystallin and Hsp27 in mammalian cells and found that expression of R120G alpha B-crystallin caused formation of inclusion bodies and co-expression of Hsp27 inhibited this formation of inclusion bodies. Clarification of physiological roles of sHSPs in degenerative diseases may lead to the development of new therapy.
Iudinkova, E. S. and S. V. Razin (2003). "[Regulatory systems of genome domains with vague boundaries]." Genetika 39(2): 182-6.
The specific features of genome domains lacking distinct boundaries are considered. These domains cannot be mapped by testing extended genome regions for nuclease sensitivity and thereby differ from structural domains determined at the level of DNA folding in chromatin. Yet they possess the properties of typical functional domains, containing a gene or several coordinated genes along with a complex of cis-regulatory elements, which control these genes. Domains with vague boundaries may be mapped with certain structural tests, e.g., by assessing histone acetylation or the distribution of tissue-specific DNase I-hypersensitive sites through extended genome regions. The mechanisms are described in detail that regulate the function of genes in domains with vague boundaries, including overlapping domains with genes differing in tissue specificity of expression.
Kelly, J. W. and W. E. Balch (2003). "Amyloid as a natural product." J Cell Biol 161(3): 461-2.
Amyloid fibrils, such as those found in Alzheimer's and the gelsolin amyloid diseases, result from the misassembly of peptides produced by either normal or aberrant intracellular proteolytic processing. A paper in this issue by Marks and colleagues (Berson et al., 2003) demonstrates that intra-melanosome fibrils are formed through normal biological proteolytic processing of an integral membrane protein. The resulting peptide fragment assembles into fibrils promoting the formation of melanin pigment granules. These results, along with the observation that amyloid fibril formation by bacteria is highly orchestrated, suggest that fibril formation is an evolutionary conserved biological pathway used to generate natural product nanostructures.
Kiefer, H. (2003). "In vitro folding of alpha-helical membrane proteins." Biochim Biophys Acta 1610(1): 57-62.
For large-scale production, as required in structural biology, membrane proteins can be expressed in an insoluble form as inclusion bodies and be refolded in vitro. This requires refolding conditions where the native form is thermodynamically stable and where nonproductive pathways leading to aggregation are avoided. Examples of successful refolding are reviewed and general guidelines to establish refolding protocols of membrane proteins are presented.
Miyata, Y. (2003). "[Molecular chaperone HSP90 as a novel target for cancer chemotherapy]." Nippon Yakurigaku Zasshi 121(1): 33-42.
HSP90 is one of the major molecular chaperones whose expression level increases by environmental stresses. Even under normal conditions, HSP90 is a highly abundant cytosolic protein and is essential for cell viability. HSP90 is involved in the maintenance of appropriate folding and conformation of many cellular functional proteins. These "HSP90 client proteins" are associated with HSP90 and they include a wide variety of signal-transducing proteins that regulate cell growth and differentiation, such as protein kinases and steroid hormone receptors. HSP90 functions in an ATP-dependent manner with other molecular chaperones such as Cdc37 and FKBP52. An HSP90 inhibitor, geldanamycin, binds the ATP-binding pocket of HSP90 and specifically inhibits the essential ATPase activity of HSP90. Thus, treatment of cells with geldanamycin results in inactivation, destabilization, and degradation of HSP90 client proteins. Because HSP90 client proteins play important roles in the regulation of the cell cycle, cell growth, cell survival, apoptosis, and oncogenesis, geldanamycin obstructs the proliferation of cultured cancer cells and shows anti-cancer activity in experimental animals. Although the precise mechanism of the effect of HSP90 inhibitors on cancer cells remains to be clarified, HSP90 inhibitors will be potential and effective cancer chemotherapeutic drugs with a unique profile. In fact, a modified geldanamycin with lower toxicity, 17-allylaminogeldanamycin (17-AAG), has been examined in phase I clinic trials with encouraging results.
Montoya, M. and E. Gouaux (2003). "Beta-barrel membrane protein folding and structure viewed through the lens of alpha-hemolysin." Biochim Biophys Acta 1609(1): 19-27.
The beta-barrel is a transmembrane structural motif commonly encountered in bacterial outer membrane proteins and pore-forming toxins (PFTs). Alpha-hemolysin (alphaHL) is a cytotoxin secreted by Staphylococcus aureus that assembles from a water-soluble monomer to form a membrane-bound heptameric beta-barrel on the surface of susceptible cells, perforating the cell membranes, leading to cell death and lysis. The mechanism of heptamer assembly, which has been studied extensively, occurs in a stepwise manner, and the structures of the initial, monomeric form and final, membrane-embedded pore are known. The toxin's ability to assemble from an aqueous, hydrophilic species to a membrane-inserted oligomer is of interest in understanding the assembly of PFTs in particular and the folding and structure of beta-barrel membrane proteins in general. Here we review the structures of the monomeric and heptamer states of LukF and alphaHL, respectively, the mechanism of toxin assembly, and the relationships between alphaHL and nontoxin beta-barrel membrane proteins.
Nagata, K. (2003). "[Therapeutic strategy for fibrotic diseases by regulating the expression of collagen-specific molecular chaperone HSP47]." Nippon Yakurigaku Zasshi 121(1): 4-14.
Through disruption of the hsp47 gene in mice, we found that HSP47, a collagen-specific molecular chaperone residing in the endoplasmic reticulum, is essential for mouse development. Improper triple helix formation was observed in hsp47-null embryos, and no collagen fibrils in the mesenchyme or basement membranes between the mesenchyme and epithelial cell layers were seen in those mice, which resulted in embryonic lethality. Interestingly, constitutive expression of HSP47 is always correlated with that of collagens in various cells or tissues. HSP47 is markedly up-regulated during the progression of fibrosis in the liver, kidney, lung, and so on. A preliminary experiment showed that down-regulation of HSP47 caused the reduction in the progression of fibrosis by down-regulating the accumulation of collagens in the tissues, which suggests a novel strategy for the therapy of fibrotic diseases including liver cirrhosis.
Opekarova, M. and W. Tanner (2003). "Specific lipid requirements of membrane proteins--a putative bottleneck in heterologous expression." Biochim Biophys Acta 1610(1): 11-22.
Membrane proteins are mostly protein-lipid complexes. For more than 30 examples of membrane proteins from prokaryotes, yeast, plant and mammals, the importance of phospholipids and sterols for optimal activity is documented. All crystallized membrane protein complexes show defined lipid-protein contacts. In addition, lipid requirements may also be transitory and necessary only for correct folding and intercellular transport. With respect to specific lipid requirements of membrane proteins, the phospholipid and glycolipid as well as the sterol content of the host cell chosen for heterologous expression should be carefully considered. The lipid composition of bacteria, archaea, yeasts, insects,Xenopus oocytes, and typical plant and mammalian cells are given in this review. A few examples of heterologous expression of membrane proteins, where problems of specific lipid requirements have been noticed or should be thought of, have been chosen.
Oppermann, U., C. Filling, et al. (2003). "Short-chain dehydrogenases/reductases (SDR): the 2002 update." Chem Biol Interact 143-144: 247-53.
Short-chain dehydrogenases/reductases (SDR) form a large, functionally heterogeneous protein family presently with about 3000 primary and about 30 3D structures deposited in databases. Despite low sequence identities between different forms (about 15-30%), the 3D structures display highly similar alpha/beta folding patterns with a central beta-sheet, typical of the Rossmann-fold. Based on distinct sequence motifs functional assignments and classifications are possible, making it possible to build a general nomenclature system. Recent mutagenetic and structural studies considerably extend the knowledge on the general reaction mechanism, thereby establishing a catalytic tetrad of Asn-Ser-Tyr-Lys residues, which presumably form the framework for a proton relay system including the 2'-OH of the nicotinamide ribose, similar to the mechanism found in horse liver ADH. Based on their cellular functions, several SDR enzymes appear as possible and promising pharmacological targets with application areas spanning hormone-dependent cancer forms or metabolic diseases such as obesity and diabetes, and infectious diseases.
Paiardini, A., R. Contestabile, et al. (2003). "Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes." Biochim Biophys Acta 1647(1-2): 214-9.
Vitamin B(6)-dependent enzymes may be grouped into five evolutionarily unrelated families, each having a different fold. Within fold type I enzymes, L-threonine aldolase (L-TA) and fungal alanine racemase (AlaRac) belong to a subgroup of structurally and mechanistically closely related proteins, which specialised during evolution to perform different functions. In a previous study, a comparison of the catalytic properties and active site structures of these enzymes suggested that they have a catalytic apparatus with the same basic features. Recently, recombinant D-threonine aldolases (D-TAs) from two bacterial organisms have been characterised, their predicted amino acid sequences showing no significant similarities to any of the known B(6) enzymes. In the present work, a comparative structural analysis suggests that D-TA has an alpha/beta barrel fold and therefore is a fold type III B(6) enzyme, as eukaryotic ornithine decarboxylase (ODC) and bacterial AlaRac. The presence of both TA and AlaRac in two distinct evolutionary unrelated families represents a novel and interesting example of convergent evolution. The independent emergence of the same catalytic properties in families characterised by completely different folds may have not been determined by chance, but by the similar structural features required to catalyse pyridoxal phosphate-dependent aldolase and racemase reactions.
Papp, S., E. Dziak, et al. (2003). "Is all of the endoplasmic reticulum created equal? The effects of the heterogeneous distribution of endoplasmic reticulum Ca2+-handling proteins." J Cell Biol 160(4): 475-9.
The endoplasmic reticulum is a heterogeneous compartment with respect to the distribution of its Ca2+-handling proteins, namely the Ca2+-binding proteins, the Ca2+ pumps and the Ca2+ release channels. The nonuniform distribution of these proteins may explain the functional heterogeneity of the endoplasmic reticulum, such as the generation of spatially complex Ca2+ signals, Ca2+ homeostasis, and protein folding and quality control.
Qian, Y. and E. Tiffany-Castiglioni (2003). "Lead-induced endoplasmic reticulum (ER) stress responses in the nervous system." Neurochem Res 28(1): 153-62.
Lead (Pb) poisoning continues to be a significant health risk because of its pervasiveness in the environment, its known neurotoxic effects in children, and potential endogenous exposure from Pb deposited in bone. New information about mechanisms by which Pb enters cells and its organelle targets within cells are briefly reviewed. Toxic effects of Pb on the endoplasmic reticulum (ER) are considered in detail, based on recent evidence that Pb induces the expression of the gene for 78-kD glucose-regulated protein (GRP78) and other ER stress genes. GRP78 is a molecular chaperone that binds transiently to proteins traversing through the ER and facilitates their folding, assembly, and transport. Models are presented for the induction of ER stress by Pb in astrocytes, the major cell type of the central nervous system, in which Pb accumulates. A key feature of the models is disruption of GRP78 function by direct Pb binding. Possible pathways by which Pb-bound GRP78 stimulates the unfolded protein response (UPR) in the ER are discussed, specifically transduction by IRE1/ATF6 and/or IRE1/JNK. The effect of Pb binding to GRP78 in the ER is expected to be a key component for understanding mechanisms of Pb-induced ER stress gene expression.
Richter-Landsberg, C. and O. Goldbaum (2003). "Stress proteins in neural cells: functional roles in health and disease." Cell Mol Life Sci 60(2): 337-49.
Heat shock proteins (HSPs) or stress proteins participate in protein synthesis, protein folding, transport and translocalization processes. Stress situations trigger a heat shock response leading to their induction. Similarly, they can be upregulated by impairment of the proteasomal degradation pathway. The upregulation of stress proteins is an important step in prevention of protein aggregation and misfolding after stress, and also is essential during development and differentiation. A number of HSPs are constitutively or inducibly expressed in the nervous system and connected to protection of nerve cells and glia. The cytoskeleton is affected by stress, and HSPs have been shown to interact with the cytoskeleton in normal cells and to assist proper assembly, spatial organization and cross-linking properties. The integrity of the cytoskeleton is disturbed in many neurodegenerative disorders, and filamentous cytoplasmic inclusion bodies, containing a variety of HSPs, are observed. This review summarizes the recent literature on the presence and induction of HSPs in neural cells, and their possible functional roles in health and disease are discussed.
Rutherford, S. L. (2003). "Between genotype and phenotype: protein chaperones and evolvability." Nat Rev Genet 4(4): 263-74.
Protein chaperones direct the folding of polypeptides into functional proteins, facilitate developmental signalling and, as heat-shock proteins (HSPs), can be indispensable for survival in unpredictable environments. Recent work shows that the main HSP chaperone families also buffer phenotypic variation. Chaperones can do this either directly through masking the phenotypic effects of mutant polypeptides by allowing their correct folding, or indirectly through buffering the expression of morphogenic variation in threshold traits by regulating signal transduction. Environmentally sensitive chaperone functions in protein folding and signal transduction have different potential consequences for the evolution of populations and lineages under selection in changing environments.
Scheeff, E. D. and J. L. Fink (2003). "Fundamentals of protein structure." Methods Biochem Anal 44: 15-39.
Schrag, J. D., D. O. Procopio, et al. (2003). "Lectin control of protein folding and sorting in the secretory pathway." Trends Biochem Sci 28(1): 49-57.
Glycan moieties are essential for folding, sorting and targeting of glycoproteins through the secretory pathway to various cellular compartments. The molecular mechanisms that underlie these processes, however, are only now coming to light. Recent crystallographic and NMR studies of proteins located in the endoplasmic reticulum (ER), Golgi complex and ER-Golgi intermediate compartment have illuminated their roles in glycoprotein folding and secretion. Calnexin and calreticulin, both ER-resident proteins, have lectin domains that are crucial for their function as chaperones. The crystal structure of the carbohydrate-recognition domain of ER-Golgi intermediate compartment (ERGIC)-53 complements the biochemical and functional characterization of the protein, confirming that a lectin domain is essential for the role of this protein in sorting and transfer of glycoproteins from the ER to the Golgi complex. The lectin domains of calnexin and ERGIC-53 are structurally similar, although there is little primary sequence similarity. By contrast, sequence similarity between ERGIC-53 and vesicular integral membrane protein (VIP36), a Golgi-resident protein, leaves little doubt that a similar lectin domain is central to the transport and/or sorting functions of VIP36. The theme emerging from these studies is that carbohydrate recognition and modification are central to mediation of glycoprotein folding and secretion.
Shastry, B. S. (2003). "Neurodegenerative disorders of protein aggregation." Neurochem Int 43(1): 1-7.
In recent years, it has become increasingly clear that many neurodegenerative diseases involve aggregation and deposition of misfolded proteins such as amyloid beta, tau, alpha-synuclein and polyglutamine containing proteins. This abnormal deposition of misfolded proteins produce malfunctioning of a distinctive set of neurons. It may also induce oxidative and endoplasmic reticulum stress and proteosomal and mitochondrial dysfunction that ultimately leads to neuronal death. While hereditary forms of disorders are caused by genetic mutations, many sporadic cases are likely to be due to genetic and environmental factors. These disorders are progressive in nature. Therefore, treatment is difficult. However, for some diseases, a growing number of treatment options such as drugs, antioxidants, cell transplantation, surgery, rehabilitation procedures and preimplantation diagnosis is available. It should be noted that many of these treatments produce unacceptable risks or adverse effects and they are of only minimal benefit for patients. In future, an understanding of the causes of protein aggregation and genetic and environmental susceptibility factors of a specific individual (or specific individual determinants) may provide a better opportunity for an effective therapeutic intervention.
Shuman, H. A. and T. J. Silhavy (2003). "The art and design of genetic screens: Escherichia coli." Nat Rev Genet 4(6): 419-31.
This article summarizes the general principles of selections and screens in Escherichia coli. The focus is on the lac operon, owing to its inherent simplicity and versatility. Examples of different strategies for mutagenesis and mutant discovery are described. In particular, the usefulness and effectiveness of simple colour-based screens are illustrated. The power of lac genetics can be applied to almost any bacterial system with gene fusions that hook any gene of interest to lacZ, which is the structural gene that encodes beta-galactosidase. The diversity of biological processes that can be studied with lac genetics is remarkable and includes DNA metabolism, gene regulation and signal transduction, protein localization and folding, and even electron transport.
Soto, C. (2003). "Unfolding the role of protein misfolding in neurodegenerative diseases." Nat Rev Neurosci 4(1): 49-60.
Stark, A., S. Sunyaev, et al. (2003). "A model for statistical significance of local similarities in structure." J Mol Biol 326(5): 1307-16.
Structural biology can provide three-dimensional structures for proteins of unknown function. When sequence or structure comparisons fail to suggest a function, insights can come from discovery of functionally important local structural patterns. Existing methods to detect such patterns lack rigorous statistics needed for widespread application. Here, we derive a formula to calculate statistical significance of the root-mean-square deviation between atoms in such patterns. When combined with a database search method, our statistics permit true functional or structural patterns in different folds to be discerned from noise. The approach is highly complementary to fold comparison for providing functional clues for new structures, and is key for the detection of recurrences of any new pattern.
Suzuki, T. and W. J. Lennarz (2003). "Hypothesis: a glycoprotein-degradation complex formed by protein-protein interaction involves cytoplasmic peptide:N-glycanase." Biochem Biophys Res Commun 302(1): 1-5.
A cytoplasmic peptide:N-glycanase has been implicated in the proteasomal degradation of newly synthesized misfolded glycoproteins that are exported from the endoplasmic reticulum to the cytosol. Recently, the gene encoding this enzyme (Png1p) was identified in yeast and shown to bind to the 26S proteasome through its interaction with a component of the DNA repair system, Rad23p. Moreover, a mouse homologue of Png1p (mPng1p), which has an extended N-terminal domain, was found to bind not only to the Rad23 protein, but also to various proteins related to the ubiquitin/proteasome pathway. An extended N-terminus of mPng1p, which is not found in yeast, contains a potential site of protein-protein interaction called the PUB/PUG domain. The PUB/PUG domain is predicted to be helix-rich and is found in various proteins that may be involved in the ubiquitin/proteasome-related pathway. This review will discuss the consequence of the deglycosylation reaction by peptide:N-glycanase in cellular processes. In addition, the potential importance of the PUB/PUG domain for the formation of a putative "glycoprotein-degradation complex" will be discussed.
Takahashi, S. (2003). "[Recent progress in protein folding research]." Seikagaku 75(1): 54-9.
Temussi, P. A., L. Masino, et al. (2003). "From Alzheimer to Huntington: why is a structural understanding so difficult?" Embo J 22(3): 355-61.
An increasing family of neurodegenerative disorders such as Alzheimer's, Parkinson's and Huntington's diseases, prion encephalopathies and cystic fibrosis is associated with aggregation of misfolded polypeptide chains which are toxic to the cell. Knowledge of the three-dimensional structure of the proteins implicated is essential for understanding why and how endogenous proteins may adopt a non-native fold. Yet, structural work has been hampered by the difficulty of handling proteins insoluble or prone to aggregation, and at the same time that is why it is interesting to study these molecules. In this review, we compare the structural knowledge accumulated for two paradigmatic misfolding disorders, Alzheimer's disease (AD) and the family of poly-glutamine diseases (poly-Q) and discuss some of the hypotheses suggested for explaining aggregate formation. While a common mechanism between these pathologies remains to be proven, a direct comparison may help in designing new strategies for approaching their study.
Thomma, B. P., B. P. Cammue, et al. (2003). "Mode of action of plant defensins suggests therapeutic potential." Curr Drug Targets Infect Disord 3(1): 1-8.
Higher vertebrates can rely both on an innate as well as an adaptive immune system for defense against invading pathogens. In contrast, plants can only employ an innate immune system that largely depends on the production of antimicrobial compounds such as plant defensins and other pathogenesis-related proteins. Plant defensins are ubiquitous, cationic, cysteine-rich plant peptides and have a folding pattern that shares high similarity to defense peptides of mammals and insects, suggesting an ancient and conserved origin. A large number of plant defensins appear to display antifungal activity. Some of these defensins have been found to interact with fungal-specific components in the plasmamembrane, resulting in membrane permeabilization. This makes them an attractive source of potential therapeutics to treat fungal infections.
Valentine, J. S. and P. J. Hart (2003). "Misfolded CuZnSOD and amyotrophic lateral sclerosis." Proc Natl Acad Sci U S A 100(7): 3617-22.
Amyotrophic lateral sclerosis (ALS) is a progressive degenerative disease of motor neurons. The inherited form of the disease, familial ALS, represents 5-10% of the total cases, and the best documented of these are due to lesions in SOD1, the gene encoding copper-zinc superoxide dismutase (CuZnSOD). The mechanism by which mutations in SOD1 cause familial ALS is currently unknown. Two hypotheses have dominated recent discussion of the toxicity of ALS mutant CuZnSOD proteins: the oligomerization hypothesis and the oxidative damage hypothesis. The oligomerization hypothesis maintains that mutant CuZnSOD proteins are, or become, misfolded and consequently oligomerize into increasingly high-molecular-weight species that ultimately lead to the death of motor neurons. The oxidative damage hypothesis maintains that ALS mutant CuZnSOD proteins catalyze oxidative reactions that damage substrates critical for viability of the affected cells. This perspective reviews some of the properties of both wild-type and mutant CuZnSOD proteins, suggests how these properties may be relevant to these two hypotheses, and proposes that these two hypotheses are not necessarily mutually exclusive.
Waters, P. J. (2003). "How PAH gene mutations cause hyper-phenylalaninemia and why mechanism matters: insights from in vitro expression." Hum Mutat 21(4): 357-69.
Mutations in the human PAH gene, which encodes phenylalanine hydroxylase are associated with varying degrees of hyperphenylalaninemia (HPA). The more severe of these manifest as a classic metabolic disease--phenylketonuria (PKU). In vitro expression analysis of PAH mutations has three major applications: 1) to confirm that a disease-associated mutation is genuinely pathogenic, 2) to assess the severity of a mutation's impact, and 3) to examine how a mutation exerts its deleterious effects on the PAH enzyme, that is, to elucidate the molecular mechanisms involved. Data on expression analysis of 81 PAH mutations in multiple in vitro systems is summarized in tabular form online at www.pahdb.mcgill.ca. A review of these findings points in particular to a prevalent general mechanism that appears to play a major role in the pathogenicity of many PAH mutations. Amino acid substitutions promote misfolding of the PAH protein monomer and/or oppose the correct assembly of monomers into the native tetrameric enzyme. The resulting structural aberrations trigger cellular defenses, provoking accelerated degradation of the abnormal protein. The intracellular steady-state levels of the mutant PAH enzyme are therefore reduced, leading to an overall decrease in phenylalanine hydroxylation within cells and thus to hyperphenylalaninemia. There is considerable scope for modulation of the enzymic and metabolic phenotypes by modification of the cellular handling--folding, assembly, and degradation--of the mutant PAH protein. This has major implications, both for our understanding of genotype-phenotype correlations and for the development of novel therapeutic approaches.
Williamson, J. R. (2003). "After the ribosome structures: how are the subunits assembled?" Rna 9(2): 165-7.
The recent structures of the ribosome and the ribosomal subunits only heighten the intrigue of trying to understand how the ribosome is assembled. Biochemical and mechanistic studies have mapped out the basic series of protein binding events that occur, but we do not yet have a clear picture of the RNA conformational changes that must accompany the protein binding. Recent studies point to roles of protein folding chaperones and RNA helicases as facilitators of ribosome assembly, but the basic process of assembly seems to be encoded in the RNA sequences and can occur for the most part spontaneously in vitro, and quite possibly in vivo as well.
Yoshida, T., M. Yohda, et al. (2003). "[Archael molecular chaperones: protein folding mechanism of the archael chaperonin]." Tanpakushitsu Kakusan Koso 48(1): 33-9.
Young, J. C. and F. U. Hartl (2003). "A stress sensor for the bacterial periplasm." Cell 113(1): 1-2.
DegS, the periplasmic stress sensor, becomes activated when its PDZ domain recognizes the improperly exposed C-terminal sequences of outer membrane porins. This interaction relieves the inhibition of the neighboring protease domain of DegS, triggering a proteolysis cascade that leads to the sigma(E)-driven expression of periplasmic chaperones.
Zhou, H. X. (2003). "Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen." J Mol Biol 329(1): 1-8.
Protein and other antigens typically have a number of different epitopes. This presents an opportunity for designing high-affinity antibodies by connecting via a flexible peptide linker two antibody fragments recognizing non-overlapping epitopes on the same antigen. The same strategy was employed in natural and designed DNA-binding proteins. According to a previous theory, the linking enhances the antigen-binding affinity over those of the individual antibody fragments (with association constants K(A) and K(B)) by p(d(0))K(B) or p(d(0))K(A), where p(d(0))=(3/4pil(p)bL)(3/2)exp(-3d(0)(2)/4l(p)bL)(1-5l(p)/4bL+ cdots, three dots, centered ) is the probability density for the end-to-end vector of the flexible linker with L residues to have a distance d(0). The predicted affinity enhancement is found to be actually approached by a bi-specific antibody against hen egg lysozyme consisting of scFv fragments of D1.3 and HyHEL-10. The wide applicability of the theory is demonstrated by diverse examples of protein-protein interactions constrained by flexible linkers.