scholarly journals Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy

Symmetry ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 273 ◽  
Author(s):  
Piotr Fabian ◽  
Katarzyna Stapor ◽  
Mateusz Banach ◽  
Magdalena Ptak-Kaczor ◽  
Leszek Konieczny ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Gaussian Function ◽  
3D Structure ◽  
Hydrophobic Core ◽  
Synergy Effect ◽  
Alternative Structures ◽  
Hydrophobic Cores ◽  
Terminal Section ◽  
High Degree ◽  
Sequence Identities

Proteins with a high degree of sequence similarity representing different structures provide a key to understand how protein sequence codes for 3D structure. An analysis using the fuzzy oil drop model was carried out on two pairs of proteins with different secondary structures and with high sequence identities. It has been shown that distributions of hydrophobicity for these proteins are approximated well using single 3D Gaussian function. In other words, the similar sequences fold into different 3D structures, however, alternative structures also have symmetric and monocentric hydrophobic cores. It should be noted that a significant change in the helical to beta-structured form in the N-terminal section takes places in the fragment much preceding the location of the mutated regions. It can be concluded that the final structure is the result of a complicated synergy effect in which the whole chain participates simultaneously.

Dissimilar sequence: similar structure of proteins

2016 ◽  
Vol 12 (3) ◽  
Author(s):  
Mateusz Banach ◽  
Leszek Konieczny ◽  
Irena Roterman
Keyword(s):  
Secondary Structure ◽  
Sequence Similarity ◽  
3D Structure ◽  
Core Structure ◽  
Hydrophobic Core ◽  
Similarity Estimation ◽  
Small Proteins ◽  
Structure Relation ◽  
The Status ◽  
Α Helix

AbstractSequence-to-structure relation is one of the major objects of the analysis of protein folding problem. The pair of two small proteins (domains) of similar structure (β-hairpin/α-helix/β-hairpin) generated by the chains of similar length (about 60 amino acids) with very low sequence similarity (15%) is the object of the comparable analysis of 3D structure. The criterion for similarity estimation is the status of polypeptide chain with respect to the hydrophobic core structure. The fuzzy oil drop model is applied to reveal the differentiated status of fragments of the well-defined secondary structure. This analysis allows the interpretation of the structure in other than the geometric form as it is made based on secondary structure classification. The two compared highly similar proteins appear to be different with respect to the hydrophobic core structure.

scholarly journals Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

2019 ◽  
Vol 476 (5) ◽  
pp. 809-826
Author(s):  
Karthik V. Rajasekar ◽  
Shuangxi Ji ◽  
Rachel J. Coulthard ◽  
Jon P. Ride ◽  
Gillian L. Reynolds ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Analytical Ultracentrifugation ◽  
De Novo ◽  
Learning Algorithm ◽  
Sequence Similarity ◽  
Homology Modelling ◽  
3D Structure ◽  
Large Family ◽  
Secreted Proteins ◽  
Self Incompatibility

Abstract SPH (self-incompatibility protein homologue) proteins are a large family of small, disulfide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy (Papaver rhoeas), but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of Escherichia coli, we expressed one member of this family, SPH15 from Arabidopsis thaliana, as a folded thioredoxin fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a β-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins: human transthyretin, bacterial TssJ and pneumolysin, with no discernible sequence similarity. The NMR-derived structure was compared with a de novo model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred de novo method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from P. rhoeas, which have only 15–18% sequence homology to SPH15. The DeepCDPred method gave models with lower discreet optimised protein energy scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes.

scholarly journals The TFIID Components Human TAFII140 andDrosophila BIP2 (TAFII155) Are Novel Metazoan Homologues of Yeast TAFII47 Containing a Histone Fold and a PHD Finger

2001 ◽  
Vol 21 (15) ◽  
pp. 5109-5121 ◽  
Author(s):  
Yann-Gaël Gangloff ◽  
Jean-Christophe Pointud ◽  
Sylvie Thuault ◽  
Lucie Carré ◽  
Christophe Romier ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Sequence Similarity ◽  
Protein A ◽  
Amino Acid Sequences ◽  
Molecular Organization ◽  
Phd Finger ◽  
Histone Fold ◽  
Histone Fold Domain ◽  
High Degree

ABSTRACT The RNA polymerase II transcription factor TFIID comprises the TATA binding protein (TBP) and a set of TBP-associated factors (TAFIIs). TFIID has been extensively characterized for yeast, Drosophila, and humans, demonstrating a high degree of conservation of both the amino acid sequences of the constituent TAFIIs and overall molecular organization. In recent years, it has been assumed that all the metazoan TAFIIs have been identified, yet no metazoan homologues of yeast TAFII47 (yTAFII47) and yTAFII65 are known. Both of these yTAFIIs contain a histone fold domain (HFD) which selectively heterodimerizes with that of yTAFII25. We have cloned a novel mouse protein, TAFII140, containing an HFD and a plant homeodomain (PHD) finger, which we demonstrated by immunoprecipitation to be a mammalian TFIID component. TAFII140 shows extensive sequence similarity toDrosophila BIP2 (dBIP2) (dTAFII155), which we also show to be a component of DrosophilaTFIID. These proteins are metazoan homologues of yTAFII47 as their HFDs selectively heterodimerize with dTAFII24 and human TAFII30, metazoan homologues of yTAFII25. We further show that yTAFII65 shares two domains with theDrosophila Prodos protein, a recently described potential dTAFII. These conserved domains are critical for yTAFII65 function in vivo. Our results therefore identify metazoan homologues of yTAFII47 and yTAFII65.

scholarly journals Nitrogen Fixation Genes in an EndosymbioticBurkholderia Strain

2001 ◽  
Vol 67 (2) ◽  
pp. 725-732 ◽  
Author(s):  
Daniela Minerdi ◽  
Renato Fani ◽  
Romina Gallo ◽  
Alessandra Boarino ◽  
Paola Bonfante
Keyword(s):  
Genomic Library ◽  
Sequence Similarity ◽  
Bacterial Genome ◽  
Fungal Spores ◽  
Mycorrhizal Fungus ◽  
Prokaryotic Genome ◽  
Arbuscular Mycorrhizal ◽  
Open Reading Frames ◽  
Genome Screening ◽  
High Degree

ABSTRACT In this paper we report the identification and characterization of a DNA region containing putative nif genes and belonging to a Burkholderia endosymbiont of the arbuscular mycorrhizal fungus Gigaspora margarita. A genomic library of total DNA extracted from the fungal spores was also representative of the bacterial genome and was used to investigate the prokaryotic genome. Screening of the library with Azospirillum brasilense nifHDKgenes as the prokaryotic probes led to the identification of a 6,413-bp region. Analysis revealed three open reading frames encoding putative proteins with a very high degree of sequence similarity with the two subunits (NifD and NifK) of the component I and with component II (NifH) of nitrogenase from different diazotrophs. The three genes were arranged in an operon similar to that shown by most archaeal and bacterial diazotrophs. PCR experiments with primers designed on theBurkholderia nifHDK genes and Southern blot analysis demonstrate that they actually belong to the genome of the G. margarita endosymbiont. They offer, therefore, the first sequence for the nif operon described for Burkholderia. Reverse transcriptase PCR experiments with primers designed on theBurkholderia nifH and nifD genes and performed on total RNA extracted from spores demonstrate that the gene expression was limited to the germination phase. A phylogenetic analysis performed on the available nifK sequences placed the endosymbioticBurkholderia close to A. brasilense.

Remarkable intron and exon sequence conservation in human and mouse homeobox Hox 1.3 genes

1989 ◽  
Vol 9 (5) ◽  
pp. 2273-2278
Author(s):  
E Tournier-Lasserve ◽  
W F Odenwald ◽  
J Garbern ◽  
J Trojanowski ◽  
R A Lazzarini
Keyword(s):  
Sequence Similarity ◽  
Gene Clusters ◽  
Binding Studies ◽  
Base Pairs ◽  
Cis Element ◽  
Multiple Transcripts ◽  
Exon Sequence ◽  
Dna Binding Studies ◽  
High Degree ◽  
Sequence Similarities

A high degree of conservation exists between the Hox 1.3 homeobox genes of mice and humans. The two genes occupy the same relative positions in their respective Hox 1 gene clusters, they show extensive sequence similarities in their coding and noncoding portions, and both are transcribed into multiple transcripts of similar sizes. The predicted human Hox 1.3 protein differs from its murine counterpart in only 7 of 270 amino acids. The sequence similarity in the 250 base pairs upstream of the initiation codon is 98%, the similarity between the two introns, both 960 base pairs long, is 72%, and the similarity in the 3' noncoding region from termination codon to polyadenylation signal is 90%. Both mouse and human Hox 1.3 introns contain a sequence with homology to a mating-type-controlled cis element of the yeast Ty1 transposon. DNA-binding studies with a recombinant mouse Hox 1.3 protein identified two binding sites in the intron, both of which were within the region of shared homology with this Ty1 cis element.

scholarly journals Cloning and Expression of cadD, a New Cadmium Resistance Gene of Staphylococcus aureus

1999 ◽  
Vol 181 (13) ◽  
pp. 4071-4075 ◽  
Author(s):  
Scott S. Crupper ◽  
Veronica Worrell ◽  
George C. Stewart ◽  
John J. Iandolo
Keyword(s):  
Staphylococcus Aureus ◽  
Resistance Gene ◽  
Sequence Similarity ◽  
Regulatory Gene ◽  
Cloning And Expression ◽  
Direct Repeats ◽  
Cadmium Resistance ◽  
Significant Similarity ◽  
High Degree ◽  
Level Resistance

ABSTRACT A cadmium resistance gene, designated cadD, has been identified in and cloned from the Staphylococcus aureusplasmid pRW001. The gene is part of a two-component operon which contains the resistance gene cadD and an inactive regulatory gene, cadX*. A high degree of sequence similarity was observed between cadD and thecadB-like gene from S. lugdunensis, but no significant similarity was found with either cadA orcadB from the S. aureus plasmids pI258 and pII147. The positive regulatory gene cadX* is identical tocadX from pLUG10 over a stretch of 78 codons beginning at the N terminus, but it is truncated at this point and inactive. Sequence analysis showed that the cadmium resistance operon resides on a 3,972-bp element that is flanked by direct repeats of IS257. The expression of cadD in S. aureus and Bacillus subtilis resulted in low-level resistance to cadmium; in contrast, cadA andcadB from S. aureus induced higher level resistance. However, when the truncated version ofcadX contained in pRW001 is complemented intrans with cadX from plasmid pLUG10, resistance increased approximately 10-fold suggesting that the cadmium resistance operons from pRW001 and pLUG10 are evolutionarily related. Moreover, the truncated version ofcadX contained in pRW001 is nonfunctional and may have been generated by deletion during recombination to acquire the cadmium resistance element.

Modelling generalisation gradients as augmented Gaussian functions

2020 ◽  
Vol 74 (1) ◽  
pp. 106-121 ◽  
Author(s):  
Jessica C Lee ◽  
Llewellyn Mills ◽  
Brett K Hayes ◽  
Evan J Livesey
Keyword(s):  
Gaussian Function ◽  
Peak Shift ◽  
Stimulus Dimension ◽  
Group Differences ◽  
Hierarchical Bayesian ◽  
Group Level ◽  
Gaussian Functions ◽  
Novel Method ◽  
Bayesian Curve Fitting ◽  
High Degree

Studying generalisation of associative learning requires analysis of response gradients measured over a continuous stimulus dimension. In human studies, there is often a high degree of individual variation in the gradients, making it difficult to draw conclusions about group-level trends with traditional statistical methods. Here, we demonstrate a novel method of analysing generalisation gradients based on hierarchical Bayesian curve-fitting. This method involves fitting an augmented (asymmetrical) Gaussian function to individual gradients and estimating its parameters in a hierarchical Bayesian framework. We show how the posteriors can be used to characterise group differences in generalisation and how classic generalisation phenomena such as peak shift and area shift can be measured and inferred. Estimation of descriptive parameters can provide a detailed and informative way of analysing human generalisation gradients.

scholarly journals Sequence of the Genome of the Temperate, Serotype-Converting,Pseudomonas aeruginosa Bacteriophage D3

2000 ◽  
Vol 182 (21) ◽  
pp. 6066-6074 ◽  
Author(s):  
Andrew M. Kropinski
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sequence Similarity ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Virus Family ◽  
Double Stranded Dna ◽  
High Degree ◽  
Phage Proteins ◽  
Reading Frames

ABSTRACT Temperate bacteriophage D3, a member of the virus familySiphoviridae, is responsible for serotype conversion in its host, Pseudomonas aeruginosa. The complete sequence of the double-stranded DNA genome has been determined. The 56,426 bp contains 90 putative open reading frames (ORFs) and four genes specifying tRNAs. The latter are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The tRNAs may function in the translation of certain highly expressed proteins from this relatively AT-rich genome. D3 proteins which exhibited a high degree of sequence similarity to previously characterized phage proteins included the portal, major head, tail, and tail tape measure proteins, endolysin, integrase, helicase, and NinG. The layout of genes was reminiscent of lambdoid phages, with the exception of the placement of the endolysin gene, which parenthetically also lacked a cognate holin. The greatest sequence similarity was found in the morphogenesis genes to coliphages HK022 and HK97. Among the ORFs was discovered the gene encoding the fucosamine O-acetylase, which is in part responsible for the serotype conversion events.

Expression of a UDPglucose pyrophosphorylase cDNA during fruit ripening of banana (Musa acuminata)

2000 ◽  
Vol 27 (12) ◽  
pp. 1151 ◽  
Author(s):  
Eng-Chong Pua ◽  
Stevenson Szu-Wei Lim ◽  
Pei Liu ◽  
Jian-Zhong Liu
Keyword(s):  
Sequence Similarity ◽  
Soluble Sugars ◽  
Transcript Abundance ◽  
Reproductive Organs ◽  
Banana Fruit ◽  
Amino Acid Residues ◽  
Promoting Effect ◽  
Udpglucose Pyrophosphorylase ◽  
Exogenous Ethylene ◽  
High Degree

We report the isolation of a banana cDNA, designated MWUGPA, encoding uridine diphosphoryl (UDP)-glucose pyrophosphorylase (UGPase, EC.2.7.7.9) that catalyses the reversible conversion between glucose 1-phosphate and UDPglucose in plants and animals. Furthermore, UGPase expression in fruit during ripening and in response to exogenous ethylene and sugars was also investigated. MWUGPA encodes a polypeptide of 467 amino acid residues and shares a high degree of sequence similarity (85–90%) with other plant UGPase homologs. In northern blot analysis, a 1.7-kb UGPase transcript was detected in both the vegetative and reproductive organs, but the former was considerably less abundant than the latter. In fruit, the level of accumulated transcripts was higher in pulp than peel at all ripening stages. Transcript abundance in both fruit tissues was relatively constant during ripen-ing, but pulp transcripts surged in the ‘more green than yellow’ category fruit when ethylene also increased. Further analysis revealed that UGPase expression in fruit was ethylene-inducible, but the response was tissue-specific, as evidenced by the promoting effect of exogenous ethylene on accumulation of UGPase transcripts in pulp but not peel. Exogenous application of sucrose and fructose also increased UGPase transcript abundance in leaf and fruit tissues, especially pulp, whereas exogenous glucose had little or no effect. The results of this study indicate that ethy-lene and soluble sugars may play a regulatory role in UGPase expression during ripening in banana fruit.

scholarly journals Downhill, Ultrafast and Fast Folding Proteins Revised

2020 ◽  
Vol 21 (20) ◽  
pp. 7632
Author(s):  
Mateusz Banach ◽  
Katarzyna Stapor ◽  
Leszek Konieczny ◽  
Piotr Fabian ◽  
Irena Roterman
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Gaussian Function ◽  
Water Environment ◽  
Mutual Arrangement ◽  
Hydrophobic Core ◽  
Spherical Micelle ◽  
Native Form ◽  
Hydrophobic Residues ◽  
Folding Process

Research on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhill. In the present work, an attempt to determine the characteristics of this group of proteins using fuzzy oil drop model is undertaken. According to the fuzzy oil drop model, a protein is a specific micelle composed of bi-polar molecules such as amino acids. Protein folding is regarded as a spherical micelle formation process. The presence of covalent peptide bonds between amino acids eliminates the possibility of free mutual arrangement of neighbors. An example would be the construction of co-micelles composed of more than one type of bipolar molecules. In the case of fast folding proteins, the amino acid sequence represents the optimal bipolarity system to generate a spherical micelle. In order to achieve the native form, it is enough to have an external force field provided by the water environment which directs the folding process towards the generation of a centric hydrophobic core. The influence of the external field can be expressed using the 3D Gaussian function which is a mathematical model of the folding process orientation towards the concentration of hydrophobic residues in the center with polar residues exposed on the surface. The set of proteins under study reveals a hydrophobicity distribution compatible with a 3D Gaussian distribution, taken as representing an idealized micelle-like distribution. The structure of the present hydrophobic core is also discussed in relation to the distribution of hydrophobic residues in a partially unfolded form.

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