Abstract:
:Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences found in the NCBI sequence databases (http://www.ncbi.nlm.nih.gov/), and our knowledge of function through a limited set of in-vitro biochemical studies. How these intersect through evolution is described in the first part of the review. In the second part, our understanding of a series of questions is addressed. This includes how sequences evolve within structures, how evolutionary processes enable structural transitions, how the folding process can change through evolution and what the fitness impacts of this might be. Moving beyond static structures, the evolution of protein kinetics (including normal modes) is discussed, as is the evolution of conformational ensembles and structurally disordered proteins. This ties back to a question of the role of neostructuralization and how it relates to selection on sequences for functions. The relationship between metastability, the fitness landscape, sequence divergence, and organismal effective population size is explored. Lastly, a brief discussion of modeling the evolution of sequences of ordered and disordered proteins is entertained.
journal_name
Genes (Basel)journal_title
Genesauthors
Siltberg-Liberles J,Grahnen JA,Liberles DAdoi
10.3390/genes2040748subject
Has Abstractpub_date
2011-10-28 00:00:00pages
748-62issue
4issn
2073-4425pii
genes2040748journal_volume
2pub_type
杂志文章相关文献
Genes文献大全abstract::The yeast Exophiala dermatitidis exhibits high resistance to γ-radiation in comparison to many other fungi. Several aspects of this phenotype have been characterized, including its dependence on homologous recombination for the repair of radiation-induced DNA damage, and the transcriptomic response invoked by acute γ-...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11101128
更新日期:2020-09-25 00:00:00
abstract::Genetic dissection of yield components and seed mineral-nutrient is crucial for understanding plant physiological and biochemical processes and alleviate nutrient malnutrition. Sesame (Sesamum indicum L.) is an orphan crop that harbors rich allelic repertoire for seed mineral-nutrients. Here, we harness this wide dive...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11101221
更新日期:2020-10-18 00:00:00
abstract:BACKGROUND:HER2 (human epidermal growth factor 2)-positive breast cancer is an aggressive type of breast cancer characterized by the overexpression of the receptor-type protein tyrosine kinase HER2 or amplification of the HER2 gene. It is commonly treated by the drug trastuzumab (Herceptin), but resistance to its actio...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10080568
更新日期:2019-07-26 00:00:00
abstract::The genus Lactobacillus includes species that may inhabit different anatomical locations in the human body, but the greatest percentage of its species are inhabitants of the gut. Lactobacilli are well known for their probiotic characteristics, although some species may become pathogenic and exert negative effects on h...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11101234
更新日期:2020-10-21 00:00:00
abstract::Meiosis yields haploid gametes following two successive divisions of a germ cell in the absence of intervening DNA replication. Balanced segregation of homologous chromosomes in Meiosis I is aided by a proteinaceous structure, the synaptonemal complex (SC). The objective of this study was to determine total average au...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes1030505
更新日期:2010-12-15 00:00:00
abstract::Pyrethroid resistance in major malaria vectors such as Anopheles funestus threatens malaria control efforts in Africa. Cytochrome P450-mediated metabolic resistance is best understood for CYP6P9 genes in southern Africa in An. funestus. However, we do not know if this resistance mechanism is spreading across Africa an...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11111314
更新日期:2020-11-05 00:00:00
abstract::Scutellaria baicalensis Georgi (Lamiaceae) is the source of the well-known traditional Chinese medicine "HuangQin" (Radix Scutellariae). Natural sources of S. baicalensis are rapidly declining due to high market demand and overexploitation. Moreover, the commercial products of Radix Scutellariae have often been found ...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes8090227
更新日期:2017-09-13 00:00:00
abstract::Despite recent genetic advances and numerous ongoing therapeutic trials, malignant melanoma remains fatal, and prognostic factors as well as more efficient treatments are needed. The development of such research strongly depends on the availability of appropriate models recapitulating all the features of human melanom...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes10070501
更新日期:2019-06-30 00:00:00
abstract::The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. Afte...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9040213
更新日期:2018-04-16 00:00:00
abstract::The Zn(II)₂Cys₆ zinc cluster gene family is a subclass of zinc-finger proteins, which are transcriptional regulators involved in a wide variety of biological processes in fungi. We performed genome-wide identification and characterization of Zn(II)₂Cys₆ zinc-cluster gene (C6 zinc gene) family in Tolypocladiumguangdong...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10030179
更新日期:2019-02-26 00:00:00
abstract::Salinity is one of the major environment factors that limits the growth of plants and the productivity of crops worldwide. It has been shown that Na+ transporters play a central role in salt tolerance and development of plants. The objective of this study was to identify Na+/H+ antiporter (NHX) genes and investigate t...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10050401
更新日期:2019-05-27 00:00:00
abstract::The homeodomain-leucine zipper (HD-Zip) transcription factor family is a key transcription factor family and unique to the plant kingdom. It consists of a homeodomain and a leucine zipper that serve in combination as a dimerization motif. The family can be classified into four subfamilies, and these subfamilies partic...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes7050019
更新日期:2016-05-17 00:00:00
abstract::Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11111348
更新日期:2020-11-13 00:00:00
abstract::Interleukin 8 (IL-8) participates in the immune response and has the function of inducing neutrophils to release lysosomal enzymes and eliminate pathogens. This study was to investigate the effect of single nucleotide mutations in the IL-8 gene promoter region on the coccidiosis resistance index. In this study, 180 in...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11050476
更新日期:2020-04-27 00:00:00
abstract::Inositol trisphosphate receptor (IP3R) mediated Ca+2 signaling is essential in determining the cell fate by regulating numerous cellular processes, including cell division and cell death. Despite extensive studies about the characterization of IP3R in cancer, the underlying molecular mechanism initiating the cell prol...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes12010034
更新日期:2020-12-29 00:00:00
abstract::The southern elephant seal Mirounga leonina is the largest phocid seal and one of the two species of elephant seals. They are listed as 'least concern' by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species 2015. Here, we have assembled the reference genome for M. leonina using the...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11020160
更新日期:2020-02-03 00:00:00
abstract::Horses have been studied for exercise function rather than food production, unlike most livestock. Therefore, the role and characteristics of tissue landscapes are critically understudied, except for certain muscles used in exercise-related studies. In the present study, we compared RNA-Seq data from 18 Jeju horse ske...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11111359
更新日期:2020-11-17 00:00:00
abstract::The prevalence of the so-called diseases of affluence, such as type 2 diabetes or hypertension, has increased dramatically in the last two generations. Although genome-wide association studies (GWAS) have discovered hundreds of genes involved in disease etiology, the sudden increase in disease incidence suggests a maj...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9080411
更新日期:2018-08-14 00:00:00
abstract::Inherited retinal degenerations are the leading cause of blindness in the working population. X-linked retinitis pigmentosa (XLRP), caused by mutations in the Retinitis pigmentosa GTPase regulator (RPGR) gene is one of the more severe forms, and female carriers of RPGR mutations have a variable presentation. A retrosp...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9120643
更新日期:2018-12-18 00:00:00
abstract::Genomic imprinting in domestic animals contributes to the variance of performance traits. However, research remains to be done on large-scale detection of epigenetic landscape of porcine imprinted loci including the GNAS complex locus. The purpose of this study was to generate porcine parthenogenetic fetuses and compr...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11010096
更新日期:2020-01-14 00:00:00
abstract::Network medicine relies on different types of networks: from the molecular level of protein⁻protein interactions to gene regulatory network and correlation studies of gene expression. Among network approaches based on the analysis of the topological properties of protein⁻protein interaction (PPI) networks, we discuss ...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes9090437
更新日期:2018-08-31 00:00:00
abstract::For medical genetic counseling, estimating the chance of a child being born with chromosome abnormality is crucially important. Cytogenetic diagnostics of parents with a balanced karyotype are a special case. Such chromosome rearrangements cannot be detected with comprehensive chromosome screening. In the current pape...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11121511
更新日期:2020-12-17 00:00:00
abstract::The histone-like nucleoid structuring protein (H-NS) has played a key role in shaping the evolution of Shigella spp., and provides the backdrop to the regulatory cascade that controls virulence by silencing many genes found on the large virulence plasmid. H-NS and its paralogue StpA are present in all four Shigella sp...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes7120112
更新日期:2016-12-01 00:00:00
abstract::Although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding DNA, this view has dramatically changed in recent years. The increase of available complete bacterial genomes has revealed that many species present abundant repetitive DNA (i.e., i...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes3040634
更新日期:2012-10-12 00:00:00
abstract::MDM4, an essential negative regulator of the P53 tumor suppressor, is frequently overexpressed in cancer cells that harbor a wild-type P53. By a mechanism based on alternative splicing, the MDM4 gene generates two mutually exclusive isoforms: MDM4-FL, which encodes the full-length MDM4 protein, and a shorter splice va...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes8020082
更新日期:2017-02-20 00:00:00
abstract::We employed Illumina 450 K Infinium microarrays to profile DNA methylation (DNAm) in neuronal nuclei separated by fluorescence-activated sorting from the postmortem orbitofrontal cortex (OFC) of heroin users who died from heroin overdose (N = 37), suicide completers (N = 22) with no evidence of heroin use and from con...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes8060152
更新日期:2017-05-30 00:00:00
abstract::EuAP2 genes are well-known for their role in flower development, a legacy of the founding member of this subfamily of transcription factors, whose mutants lacked petals in Arabidopsis. However, studies of euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other as...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes10120994
更新日期:2019-12-01 00:00:00
abstract::GOLDEN2-LIKE (GLK) is a member of the myeloblastosis (MYB) family transcription factor and it plays an important role in the regulation of plastid development and stress tolerance. In this study, a gene named AhGLK1b was identified from a cultivated peanut showing down-regulation in response to low calcium with a comp...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11030343
更新日期:2020-03-24 00:00:00
abstract::White spot syndrome virus (WSSV), one of the major pathogens of Procambarus clarkii, has caused severe disruption to the aquaculture industry of P. clarkii in China. To reveal the gene regulatory mechanisms underlying WSSV infection, a comparative transcriptome analysis was performed among WSSV-infected susceptible in...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes8110320
更新日期:2017-11-10 00:00:00
abstract::Mitochondrial dynamics are known to have an important role in so-called age-related diseases, including cancer. Mitochondria is an organelle involved in many key cellular functions and responds to physiologic or stress stimuli by adapting its structure and function. Perhaps the most important structural changes involv...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes9020115
更新日期:2018-02-21 00:00:00