Abstract:
:A protein is usually classified into one of the following five structural classes: alpha, beta, alpha + beta, alpha/beta, and zeta (irregular). The structural class of a protein is correlated with its amino acid composition. However, given the amino acid composition of a protein, how may one predict its structural class? Various efforts have been made in addressing this problem. This review addresses the progress in this field, with the focus on the state of the art, which is featured by a novel prediction algorithm and a recently developed database. The novel algorithm is characterized by a covariance matrix that takes into account the coupling effect among different amino acid components of a protein. The new database was established based on the requirement that the classes should have (1) as many nonhomologous structures as possible, (2) good quality structure, and (3) typical or distinguishable features for each of the structural classes concerned. The very high success rate for both the training-set proteins and the testing-set proteins, which has been further validated by a simulated analysis and a jackknife analysis, indicates that it is possible to predict the structural class of a protein according to its amino acid composition if an ideal and complete database can be established. It also suggests that the overall fold of a protein is basically determined by its amino acid composition.
journal_name
Crit Rev Biochem Mol Bioljournal_title
Critical reviews in biochemistry and molecular biologyauthors
Chou KC,Zhang CTdoi
10.3109/10409239509083488subject
Has Abstractpub_date
1995-01-01 00:00:00pages
275-349issue
4eissn
1040-9238issn
1549-7798journal_volume
30pub_type
杂志文章,评审abstract::Following a brief introduction of cellular response to stimulation comprising leukocyte activation, three major areas are discussed: (1) the neutrophil oxidase; (2) myeloperoxidase (MPO)-dependent oxidative microbicidal reactions; and (3) MPO-independent oxidative reactions. Topics included in section (A) are current ...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238909082555
更新日期:1989-01-01 00:00:00
abstract::Some asparagine and glutamine residues in proteins undergo deamidation to aspartate and glutamate with rates that depend upon the sequence and higher-order structure of the protein. Functional groups within the protein can catalyze this reaction, acting as general acids, bases, or stabilizers of the transition state. ...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409239109081719
更新日期:1991-01-01 00:00:00
abstract::The spontaneous and unregulated polymerization of actin filaments is inhibited in cells by actin monomer-binding proteins such as profilin and Tbeta4. Eukaryotic cells and certain pathogens use filament nucleators to stabilize actin polymerization nuclei, whose formation is rate-limiting. Known filament nucleators inc...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409230903277340
更新日期:2009-11-01 00:00:00
abstract::Low-copy nuclear genes in plants are a rich source of phylogenetic information. They hold a great potential to improve the robustness of phylogenetic reconstruction at all taxonomic levels, especially where universal markers such as cpDNA and nrDNA are unable to generate strong phylogenetic hypotheses. Low-copy nuclea...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409230290771474
更新日期:2002-01-01 00:00:00
abstract::Adaptive mutation is a generic term for processes that allow individual cells of nonproliferating cell populations to acquire advantageous mutations and thereby to overcome the strong selective pressure of proliferation-limiting environmental conditions. Prerequisites for an occurrence of adaptive mutation are that th...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409230701507773
更新日期:2007-07-01 00:00:00
abstract::S-Acylation (commonly referred to as S-palmitoylation) is a post-translational modification consisting in the covalent attachment of an acyl chain to a cysteine residue of the target protein. The lability of the resulting thioester bond gives S-acylation an essential characteristic: its reversibility. S-acylation dyna...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409238.2018.1488804
更新日期:2018-08-01 00:00:00
abstract::Receptor for advanced glycation end products (RAGE) is an immunoglobulin-like receptor present on cell surface. RAGE binds to an array of structurally diverse ligands, acts as a pattern recognition receptor (PRR) and is expressed on cells of different origin performing different functions. RAGE ligation leads to the i...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章
doi:10.1080/10409238.2020.1819194
更新日期:2020-12-01 00:00:00
abstract::Torsin ATPases (Torsins) belong to the widespread AAA+ (ATPases associated with a variety of cellular activities) family of ATPases, which share structural similarity but have diverse cellular functions. Torsins are outliers in this family because they lack many characteristics of typical AAA+ proteins, and they are t...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238.2015.1091804
更新日期:2015-01-01 00:00:00
abstract::Small regulatory RNAs can modify the activity of proteins and the stability and translation of mRNAs. They have now been found in a wide range of organisms, and can play previously unsuspected critical regulatory roles. The bacterial small RNAs include two major classes. The largest family(with at least 20 members in ...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409230590918702
更新日期:2005-03-01 00:00:00
abstract::RNA helicases represent a large family of proteins that have been detected in almost all biological systems where RNA plays a central role. They are ubiquitously distributed over a wide range of organisms and are involved in nuclear and mitochondrial splicing processes, RNA editing, rRNA processing, translation initia...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409239891204233
更新日期:1998-01-01 00:00:00
abstract::The discovery that SRA RNA can function as a nuclear receptor (NR) coactivator resulted in a fundamental change in the perception of how NRs and their coregulators may regulate hormone signaling pathways. The subsequent identification of molecules capable of binding SRA, including SHARP, p68, and more recently SLIRP, ...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409230802661719
更新日期:2009-01-01 00:00:00
abstract::The purpose of this review is to provide an analysis of the latest developments on the functions of the carbon catabolite-repression 4-Not (Ccr4-Not) complex in regulating eukaryotic gene expression. Ccr4-Not is a nine-subunit protein complex that is conserved in sequence and function throughout the eukaryotic kingdom...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238.2012.667214
更新日期:2012-07-01 00:00:00
abstract::The nicotinic acetylcholine receptor (nAcChR) is a ligand-gated ion channel found in the postsynaptic membranes of electric organs, at the neuromuscular junction, and at nicotinic cholinergic synapses of the mammalian central and peripheral nervous system. The nAcChR from Torpedo electric organ and mammalian muscle is...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238909082553
更新日期:1989-01-01 00:00:00
abstract::The mevalonate-isoprenoid-cholesterol biosynthesis pathway plays a key role in human health and disease. The importance of this pathway is underscored by the discovery that two major isoprenoids, farnesyl and geranylgeranyl pyrophosphate, are required to modify an array of proteins through a process known as protein p...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409238.2018.1458070
更新日期:2018-06-01 00:00:00
abstract::Glycosaminoglycans (GAGs) play an intricate role in the extracellular matrix (ECM), not only as soluble components and polyelectrolytes, but also by specific interactions with growth factors and other transient components of the ECM. Modifications of GAG chains, such as isomerization, sulfation, and acetylation, gener...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409239509083490
更新日期:1995-01-01 00:00:00
abstract::This review focuses on how microbes live on CO as a sole source of carbon and energy and with CO by generating carbon monoxide as a metabolic intermediate. The use of CO is a property of organisms that use the Wood-L jungdahl pathway of autotrophic growth. The review discusses when CO metabolism originated, when and h...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409230490496577
更新日期:2004-05-01 00:00:00
abstract::The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literatur...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409230490460765
更新日期:2004-03-01 00:00:00
abstract::Our understanding of the fundamental regulatory roles that tyrosine phosphatases play within cells has advanced significantly in the last two decades. Out-dated ideas that tyrosine phosphatases acts solely as the "off" switch counterbalancing the action of tyrosine kinases has proved to be flawed. PTP1B is the most ch...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238.2013.819830
更新日期:2013-09-01 00:00:00
abstract::Activation of cell growth leads to the multiple phosphorylation of 40S ribosomal protein S6. The kinase responsible for controling this event is termed p70s6k/p85s6k. Both isoforms of the kinase are derived from a common gene activated by a complex set of phosphorylation events; each resides in a unique cellular compa...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409239409083485
更新日期:1994-01-01 00:00:00
abstract::Type 1 protein phosphatases (PP-1) comprise a group of widely distributed enzymes that specifically dephosphorylate serine and threonine residues of certain phosphoproteins. They all contain an isoform of the same catalytic subunit, which has an extremely conserved primary structure. One of the properties of PP-1 that...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409239209082564
更新日期:1992-01-01 00:00:00
abstract::HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) RNases are an emerging class of functionally diverse RNA processing and degradation enzymes. Members are defined by a small α-helical bundle encompassing a short consensus RNase motif. HEPN dimerization is a universal requirement for RNase activation as the c...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章
doi:10.1080/10409238.2020.1856769
更新日期:2021-02-01 00:00:00
abstract::We know of three routes that organisms have evolved to synthesize complex organic molecules from CO2: the Calvin cycle, the reverse tricarboxylic acid cycle, and the reductive acetyl-CoA pathway. This review describes the enzymatic steps involved in the acetyl-CoA pathway, also called the Wood pathway, which is the ma...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409239109114070
更新日期:1991-01-01 00:00:00
abstract::The eukaryotic MCM2-7 complex is recruited onto origins of replication during the G1 phase of the cell cycle and acts as the main helicase at the replication fork during the S phase. Over the last few years a number of structural reports on MCM proteins using both electron microscopy and protein crystallography have b...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409230903186012
更新日期:2009-09-01 00:00:00
abstract::O-linked β-N-acetylglucosamine (O-GlcNAc) is a regulatory post-translational modification of intracellular proteins. The dynamic and inducible cycling of the modification is governed by O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) in response to UDP-GlcNAc levels in the hexosamine biosynthetic pathway (HBP). Due t...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238.2014.884535
更新日期:2014-03-01 00:00:00
abstract::Ribonucleotides are the most abundant non-canonical nucleotides in the genome. Their vast presence and influence over genome biology is becoming increasingly appreciated. Here we review the recent progress made in understanding their genomic presence, incorporation characteristics and usefulness as biomarkers for poly...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章
doi:10.1080/10409238.2020.1869175
更新日期:2021-02-01 00:00:00
abstract::Serotonin receptors are the product of 15 distinct genes, 14 of which are G protein-coupled receptors. These receptors are expressed in a wide range of cell types, including distinct neuronal populations, and promote diverse functional responses in multiple organ systems. These receptors are important for mediating th...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238.2010.516741
更新日期:2010-12-01 00:00:00
abstract::DNA double-strand breaks are highly toxic DNA lesions that cause genomic instability, if not efficiently repaired. RecQ helicases are a family of highly conserved proteins that maintain genomic stability through their important roles in several DNA repair pathways, including DNA double-strand break repair. Double-stra...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238.2014.942450
更新日期:2014-11-01 00:00:00
abstract::All living organisms depend on dynamic mechanisms that repeatedly reassess the status of amassed energy, in order to adapt energy supply to demand. The AMP-activated protein kinase (AMPK) alphabetagamma heterotrimer has emerged as an important integrator of signals managing energy balance. Control of AMPK activity inv...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238.2010.488215
更新日期:2010-08-01 00:00:00
abstract::The unfolded protein response (UPR) is induced when the quality control machinery of the cell is overloaded with unfolded proteins or when one of the functions of the endoplasmic reticulum (ER) is perturbed. Here, I describe UPR in yeast and mammals, and compare it to what we know about pathogenic fungi and the parasi...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.3109/10409238.2015.1042541
更新日期:2015-01-01 00:00:00
abstract::Insulin-degrading enzyme (IDE) is a ubiquitous zinc peptidase of the inverzincin family, which has been initially discovered as the enzyme responsible for insulin catabolism; therefore, its involvement in the onset of diabetes has been largely investigated. However, further studies on IDE unraveled its ability to degr...
journal_title:Critical reviews in biochemistry and molecular biology
pub_type: 杂志文章,评审
doi:10.1080/10409238.2017.1337707
更新日期:2017-10-01 00:00:00