Abstract:
:In this work, we present an extensive analysis of protein contact network topology applied to a wide data set. We extended the concept of degree distribution to graphlets, describing local connectivity patterns. We compared results to those derived from artificial networks of the same size (number of nodes), reproducing the average degree of each protein network. The artificial networks resemble the coiling of immaterial cords and we tried to understand if they could catch the protein structure topology upon the sole constraint of backbone (cord). We found a surprisingly similar pattern for local topological descriptors (graphlets distribution) while real proteins and cords differ at large extent in the global topological invariant average shortest path that presumably catches the systemic nature of protein and the non negligible encumbrance of backbone (residues steric hindrance). We demonstrated average shortest path to link polymer length and physical size of the molecule, and its minimization plays the role of `target function` of folding process.
journal_name
Curr Protein Pept Scijournal_title
Current protein & peptide scienceauthors
Santoni D,Paci P,Di Paola L,Giuliani Adoi
10.2174/138920371701151130203441subject
Has Abstractpub_date
2016-01-01 00:00:00pages
26-9issue
1eissn
1389-2037issn
1875-5550pii
CPPS-EPUB-70598journal_volume
17pub_type
杂志文章abstract::The affinity tags are unique proteins/peptides that are attached at the N- or C-terminus of the recombinant proteins. These tags help in protein purification. Additionally, some affinity tags also serve a dual purpose as solubility enhancers for challenging protein targets. By applying a combinatorial approach, carefu...
journal_title:Current protein & peptide science
pub_type: 杂志文章
doi:10.2174/1389203721666200606220109
更新日期:2020-01-01 00:00:00
abstract::Fbxo7/PARK15 has well-defined roles, acting as part of a Skp1-Cul1-F box protein (SCF)- type E3 ubiquitin ligase and also having SCF-independent activities. Mutations within FBXO7 have been found to cause an early-onset Parkinson's disease, and these are found within or near to its functional domains, including its F-...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203717666160311121433
更新日期:2017-01-01 00:00:00
abstract::The field of bioinformatics has become a major part of the drug discovery pipeline playing a key role in improvement and acceleration of this time and money consuming process. Here we review the application of the informational spectrum method (ISM), a virtual spectroscopy method for structure/function analysis of pro...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920308785915245
更新日期:2008-10-01 00:00:00
abstract::Protein-protein interaction (PPI) is necessary for most of the biological processes and requisite for host-pathogen communication. Most of the threatening human diseases are caused by different types of interactions of proteins with their prior infected proteins or with pathogen's proteins. Understanding of involved m...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203718666170828122927
更新日期:2018-01-01 00:00:00
abstract::The cytolysin is a novel, two-peptide lytic toxin produced by some strains of Enterococcus faecalis. It is toxic in animal models of enterococcal infection, and associated with acutely terminal outcome in human infection. The cytolysin exerts activity against a broad spectrum of cell types including a wide range of gr...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203053027557
更新日期:2005-02-01 00:00:00
abstract::Pathogenic aggregation is closely associated with various protein misfolding diseases such as type 2 diabetes mellitus and Alzheimer's disease. Amyloidogenic proteins that have a propensity to assemble into amyloid oligomers and fibrils form the aggregates. The tumor suppressor p53, a transcription factor that regulat...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:
更新日期:2015-01-01 00:00:00
abstract::Serine proteinases fulfill and facilitate a broad spectrum of biological processes. They are held in check by different specific inhibitors. This delicate balance can be disturbed by genetic defects or exogenous influences and has been shown as the underlying or promoting cause for a large number of different diseases...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203054065374
更新日期:2005-06-01 00:00:00
abstract::There has been a tremendous increase in the number of approved drugs derived from recombinant proteins; however, their development as potential drugs has been hampered by their instability that causes difficulty to formulate them as therapeutic agents. It has been shown that the reactivity of thiol and disulfide funct...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920309789630534
更新日期:2009-12-01 00:00:00
abstract::The plasma membrane Ca2+ ATPases (PMCAs) are responsible for the clearance of Ca2+ out of cells after intracellular Ca2+ transients. Cooperating with Na+/Ca2+ exchangers (NCXs) and Ca2+ buffering proteins, PMCAs play an essential role in maintaining the long-term cellular Ca2+ homeostasis. The plasma membrane Ca2+ ATP...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203719666180416122745
更新日期:2018-01-01 00:00:00
abstract::STATs promote fundamental cellular processes, marking them as convergence points of many oncogenic and inflammatory pathways. Therefore, aberrant activation of STAT signaling is implicated in a plethora of human diseases, like cancer, inflammation and auto-immunity. Identification of STAT-specific inhibitors is the to...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203716666151102103706
更新日期:2016-01-01 00:00:00
abstract::Naturally occurring protease inhibitors (PI) of the Bowman-Birk type constitute a major PI family in cereal and legume seeds. The family name is derived from the names of the two investigators who characterised the first inhibitor of this type, the Bowman-Birk inhibitor from soybean (BBI). These proteins have the capa...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920306777452349
更新日期:2006-06-01 00:00:00
abstract::Parvalbumin (PA) is a classical small, mostly cytosolic Ca2+-binding protein of the EF-hand superfamily expressed in vertebrates in a tissue- and cell-specific manner, serving as a magnesium/ calcium buffer. In the last decade novel data were published on structural peculiarities of PA, likely affecting its functional...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203717666161213115746
更新日期:2017-01-01 00:00:00
abstract::Cardiovascular diseases (CVDs) are the leading cause of mortality worldwide. Rehmanniae Radix Praeparata (RRP) is a popular medicinal herb widely used in traditional Chinese medicine (TCM) to treat CVDs. However, the development of this novel therapeutic product has been stagnant, and its molecular mechanism of action...
journal_title:Current protein & peptide science
pub_type: 杂志文章
doi:10.2174/1389203720666190610161535
更新日期:2019-01-01 00:00:00
abstract::The Mastermind-like (MAML) proteins are transcriptional coactivators for Notch signaling, an evolutionarily conserved pathway that plays several key roles in development and in human disease. The MAML family contains MAML1, MAML2, and MAML3. More recently, MAML1 has been shown to function as a coactivator for the tumo...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920309789630543
更新日期:2009-12-01 00:00:00
abstract::Tribbles homolog 3 (TRIB3) is a mammalian gene that is upregulated in response to several types of cell death-inducing cellular stress. The TRIB3 protein is a pseudokinase, a protein kinase-like scaffold with impaired catalytic activity. However, research has revealed it to be prolific at forming protein- protein inte...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203718666170406124547
更新日期:2017-01-01 00:00:00
abstract::The needs for purified nucleic acids for preparative and analytical applications have increased constantly, demanding for the development of new and more efficient methods for their recovery and isolation. DNA molecules harbour some intrinsic chemical properties that render them suitable for chromatographic separation...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203718666171024112556
更新日期:2019-01-01 00:00:00
abstract::To defend themselves from attack by pathogens, plants can rely only on their innate defense systems. Defensins are antimicrobial peptides that contribute to plant immunity by displaying a direct cidal activity against various pathogens, some of which are responsible for plant diseases. These determine a significant de...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920310791112101
更新日期:2010-05-01 00:00:00
abstract::Mites and ticks are associated with many human diseases including allergic diseases and scabies. With the recent advances in the high throughput DNA sequencing technology, many mitochondrial nuclear genomes of these species have been sequenced and the resulting genomic resources will certainly provide novel insights f...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203720666190719150432
更新日期:2020-01-01 00:00:00
abstract::The bioactive peptides are protein fragments which have a positive impact on the intestinal homeostasis. Intestinal homeostasis depends on the diverse functions of intestinal barrier including the microbiological, physical, chemical and immunological barriers. Defects in intestinal barrier function are associated with...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203716666150630134804
更新日期:2015-01-01 00:00:00
abstract::Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-i...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920311796957667
更新日期:2011-09-01 00:00:00
abstract::The epidermal growth factor receptor (EGFR) belongs to ErbB family of tyrosine kinases, which plays an important role in the regulation of cell proliferation, survival, differentiation, and metastasis. In addition, tumors develop resistance to EGFR inhibitors due to the presence or development of point mutations in th...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203718666170106104211
更新日期:2018-02-13 00:00:00
abstract::The High mobility group box 1 (HMGB1) protein is an extremely versatile, highly conserved nuclear protein, with its unique intracellular and extracellular functions mediated by its relatively simple domain structure. Within the nucleus, HMGB1 binds to DNA minor groove in a nonspecific manner and causes bends in the do...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203717666160226145217
更新日期:2016-01-01 00:00:00
abstract::A growing body of work demonstrates the importance of post-transcriptional control, in particular translation initiation, in the overall regulation of gene expression. Here we focus on the contribution of regulatory elements within the 5' and 3' untranslated regions of mRNA to gene expression in eukaryotic cells inclu...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920312801619475
更新日期:2012-06-01 00:00:00
abstract::In spite of the relevance of the results obtained through the clinical application of chemotherapeutic agents (reverse transcriptase and proteinase inhibitors) that are able to prolong the life span of affected people, acquired immunodeficiency syndrome (AIDS) remains a serious and lethal disease. AIDS is caused by a ...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203043379729
更新日期:2004-08-01 00:00:00
abstract::Calmodulin (CaM) is a highly conserved eukaryotic Ca2+ sensor protein that is able to bind a large variety of target sequences without a defined consensus sequence. The recognition of this diverse target set allows CaM to take part in the regulation of several vital cell functions. To fully understand the structural b...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203720666190925101937
更新日期:2019-01-01 00:00:00
abstract::Hemoglobin (Hb) is the prototypical example of a cooperative protein. Cooperativity of Hb is largely accounted for by the oxygen-linked allosteric interconversion between the T and R states/structures. Allostery is such a powerful explanation of Hb cooperativity that the possibility of cooperative events occurring wit...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203718666171030103310
更新日期:2018-01-01 00:00:00
abstract::Cardiovascular (CV) diseases are caused by vascular dysfunction. The enhanced sensitivity to vasoconstrictors, reduced endothelium-derived vasodilators nitric oxide (NO) and prostacyclin (PGI2), and endothelium-derived hyperpolarization (EDH) indicate CV dysfunction. In recent years, recombinant human relaxin, known a...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203719666180709103020
更新日期:2018-01-01 00:00:00
abstract::Despite a wide variety of biological functions, alpha-helical membrane proteins display a rather simple transmembrane architecture. Although not many high resolution structures of transmembrane proteins are available today, our understanding of membrane protein folding has emerged in the recent years. Now we begin to ...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920307779941578
更新日期:2007-02-01 00:00:00
abstract::The aggregation of proteins or their digested fragments through β-sheet structures has a great significance because it leads to neurodegenerative diseases, which are a problem of the aging societies of the developed countries. Short peptides are typically used as models to study the formation of specific structures. H...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/1389203718666170516111601
更新日期:2017-01-01 00:00:00
abstract::By utilizing recently developed full-length cDNA technologies, large-scale cDNA sequencing was carried out by several cDNA projects. Now full-length cDNA resources cover the major part of the protein-coding human genes. Comprehensive analyses of the collected full-length cDNA data revealed not only the complete sequen...
journal_title:Current protein & peptide science
pub_type: 杂志文章,评审
doi:10.2174/138920306776359795
更新日期:2006-04-01 00:00:00