Abstract Background Plant n on- s pecific l ipid t ransfer p roteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating plant defence activity against bacterial fungal pathogens, enhancing cell wall extension tobacco. However, the lipid transfer mechanism of is still unclear, comprehensive information difficult to obtain. Methods In this study, we identified 595 from 121...

Circular permutation (CP) in a protein can be considered as if its sequence were circularized followed by creation of termini at new location. Since the first observation CP 1979, substantial number studies have concluded that circular permutants (CPs) usually retain native structures and functions, sometimes with increased stability or functional diversity. Although this interesting property has made useful many engineering folding researches, large-scale collections CP-related information...

The knowledge of conserved sequences in proteins is valuable identifying functionally or structurally important residues. Generating the conservation profile a sequence requires aligning families homologous and having their evolutionary relationships. Here, we report that at residue level can be quantitatively derived from single protein structure with only backbone information. We found reciprocal packing density profiles structures closely resemble profiles. For set 554 nonhomologous...

Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed reduce three-dimensional protein structures one-dimensional text strings then analyzed by traditional sequence alignment methods; however, accuracy is usually sacrificed speed still unable match tools. Here, we aimed linear encoding methodology develop efficient can...

Circular permutation of a protein can be visualized as if the original amino- and carboxyl termini were linked new ones created elsewhere. It has been well-documented that circular permutants usually retain native structures biological functions. Here we report CPSARST (Circular Permutation Search Aided by Ramachandran Sequential Transformation) to an efficient database search tool. In this post-genomics era, when amount structural data is increasing exponentially, it provides way rapidly...

Circular permutation (CP) is a protein structural rearrangement phenomenon, through which nature allows homologs to have different locations of termini and thus varied activities, stabilities functional properties. It can be applied in many fields research bioengineering. The limitation applying CP lies its technical complexity, high cost uncertainty the viability resulting variants. Not every position used create viable circular permutant, but there still lack practical computational tools...

Split-protein systems have emerged as a powerful tool for detecting biomolecular interactions and reporting biological reactions. However, reliable methods identifying viable split sites are still unavailable. In this study, we demonstrated the feasibility that valid circular permutation (CP) in proteins potential to act CP prediction can be used search internal permissive creating new proteins. Using protein ligase, intein, model, predictor facilitated creation of permutants which backbone...

iSARST is a web server for efficient protein structural similarity searches. It multi-processor, batch-processing and integrated implementation of several comparison tools two database searching methods: SARST common homologs CPSARST with circular permutations. allows users submitting multiple PDB/SCOP entry IDs or an archive file containing many structures. After scanning the target using SARST/CPSARST, ordering hits are refined conventional structure alignment such as FAST, TM-align SAMO,...

Circular permutation (CP) refers to situations in which the termini of a protein are relocated other positions structure. CP occurs naturally and has been artificially created study function, stability folding. Recently is increasingly applied engineer enzyme structure create bifunctional fusion proteins unachievable by tandem fusion. complicated expensive technique. An intrinsic difficulty its application lies fact that not every position amenable for creating viable permutant. To examine...

Protein secondary structure prediction (SSP) has a variety of applications; however, there been relatively limited improvement in accuracy for years. With vision moving forward all related fields, we aimed to make fundamental advance SSP. There have many admirable efforts made improve the machine learning algorithm This work thus took step back by manipulating input features. A element-based position-specific scoring matrix (SSE-PSSM) is proposed, based on which new set features can be...

Secondary structure prediction (SSP) of proteins is an important structural biology technique with many applications. There have been ~300 algorithms published in the past seven decades fierce competition accuracy. In first 60 years, accuracy three-state SSP rose from ~56% to 81%; after that, it has long stayed at 81–86%. 1990s, theoretical limit had estimated be 88%. Thus, now generally considered not challenging or too improve. However, we found that might underestimated. Besides, there...

Inhibitory control is a cognitive process that inhibits response. It used in everyday activities, such as driving motorcycle, car and playing game. The effect of this can be compared to the red traffic light real world. In study, we investigated brain connectivity under human inhibitory using phase lag index inter-trial coherence (ITC). gives more accurate representation functional neural network. Results electroencephalography (EEG), data sets were generated from twelve healthy subjects...

This work presents a novel detection method for three-dimensional domain swapping (DS), mechanism forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” and exchanged the opened portion to form intertwined oligomers. Since first report of DS in mid 1990s, an increasing number identified cases has led postulation might occur with unconstrained terminus under appropriate conditions. may play important roles molecular evolution functional...

Abstract Background Microorganisms able to grow under artificial culture conditions comprise only a small proportion of the biosphere's total microbial community. Until recently, scientists have been unable perform thorough analyses difficult-to-culture microorganisms due limitations in sequencing technology. As modern techniques dramatically increased rates and rapidly expanded number sequenced genomes, addition traditional taxonomic classifications which focus on evolutionary relationships...

The secondary structure prediction of proteins is a classic topic computational structural biology with variety applications. During the past decade, accuracy achieved by state-of-the-art algorithms has been >80%; meanwhile, time cost increased rapidly because exponential growth fundamental protein sequence data. Based on literature studies and preliminary observations relationships between size/homology dataset speed/accuracy predictions, we raised two hypotheses that might be helpful to...

Hepatoma-derived growth factor (hHDGF) and HDGF-related proteins (HRPs) contain conserved N-terminal HATH domains with a characteristic structural motif, namely the PWWP motif. The domain has attracted attention because of its ability to bind heparin/heparan sulfate, DNA, methylated histone peptide. Depending on sequence HRP HATHs are classified into P-type (Pro-His-Trp-Pro) A-type (Ala-His-Trp-Pro) forms. is highly unstable tends precipitate in solution. We replaced Pro residue HATHHDGF Ala...

The secondary structure prediction (SSP) of proteins has long been an essential structural biology technique with various applications. Despite its vital role in many research and industrial fields, recent years, as the accuracy state-of-the-art predictors approaches theoretical upper limit, SSP considered no longer challenging or too to make advances. With belief that substantial improvement will move forward fields depending on it, we conducted this study, which focused three issues have...

Abstract Background This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent connecting the native termini of followed by creating at another site. Although CP has been applied in many fields, its implementation is still costly because inevitable trials and errors. Results Here we present CirPred, structure modeling linker design method for circularly permuted proteins. Compared with...