Background: Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein structures, and the more general cases of non-cyclic permutations between similar structures, which are related by non-topological rearrangement beyond circular permutation. We present a method based on an approximation algorithm that finds sequence-order independent structural alignments that are close to optimal. We formulate the structural alignment problem as a special case of the maximum-weight independent set problem, and solve this computationally intensive problem approximately by iteratively solving relaxations of a corresponding integer programming problem. The resulting structural alignment is sequence order independent. Our method is also insensitive to insertions, deletions, and gaps.
Results: Using a novel similarity score and a statistical model for significance p-value, we are able to discover previously unknown circular permuted proteins between nucleoplasmin-core protein and auxin binding protein, between aspartate rasemase and 3-dehydrogenate dehydralase, as well as between migration inhibition factor and arginine repressor which involves an additional strand-swapping. We also report the finding of non-cyclic permuted protein structures existing in nature between AML1/core binding factor and ribofalvin synthase. Our method can be used for large scale alignment of protein structures regardless of the topology.
Conclusion: The approximation algorithm introduced in this work can find good solutions for the problem of protein structure alignment. Furthermore, this algorithm can detect topological differences between two spatially similar protein structures. The alignment between MIF and the arginine repressor demonstrates our algorithm's ability to detect structural similarities even when spatial rearrangement of structural units has occurred. The effectiveness of our method is also demonstrated by the discovery of previously unknown circular permutations. In addition, we report in this study the finding of a naturally occurring non-cyclic permuted protein between AML1/Core Binding Factor chain F and riboflavin synthase chain A.
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http://dx.doi.org/10.1186/1471-2105-8-388 | DOI Listing |
Arch Microbiol
January 2025
Department of Botany, CMS College Kottayam, Kottayam, Kerala, 686001, India.
Among all photosynthetic life forms, cyanobacteria exclusively possess a water-soluble, light-sensitive carotenoprotein complex known as orange carotenoid proteins (OCPs), crucial for their photoprotective mechanisms. These protein complexes exhibit both structural and functional modularity, with distinct C-terminal (CTD) and N-terminal domains (NTD) serving as light-responsive sensor and effector regions, respectively. The majority of cyanobacterial genomes contain genes for OCP homologs and related proteins, highlighting their essential role in survival of the organism over time.
View Article and Find Full Text PDFCell Mol Biol (Noisy-le-grand)
January 2025
Dept. of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh.
Rice salt tolerance is highly anticipated to meet global demand in response to decreasing farmland and soil salinization. Therefore, dissecting the genetic loci controlling salt tolerance in rice for improving productivity is of utmost importance. Here, we evaluated six salt-tolerance-related traits of a biparental mapping population comprising 280 F2 rice individuals (Oryza sativa L.
View Article and Find Full Text PDFCell Mol Biol (Noisy-le-grand)
January 2025
College of Life Sciences, Liaoning Normal University, Dalian 116000, Liaoning Province, China.
Liaoning cashmere goat is an outstanding breed in China primarily for cashmere production, with strict controls against genetic outflow. Melatonin(MT) is a key factor affecting cashmere growth, and preliminary transcriptome sequencing indicated that melatonin upregulates the expression of the PIP5K1A gene in skin fibroblasts. To predict the physicochemical properties of PIP5K1A in Liaoning cashmere goats, ascertain the tissue localization of PIP5K1A in their skin, and explore the role and mechanism of PIP5K1A in the proliferation of skin fibroblasts.
View Article and Find Full Text PDFXi Bao Yu Fen Zi Mian Yi Xue Za Zhi
January 2025
Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China. *Corresponding authors, E-mail:
B and T lymphocyte attenuator (BTLA) is an inhibitory immune checkpoint, which typically interacts with herpesvirus entry mediator (HVEM) and plays a crucial role in regulating immune balance. BTLA interacts with its ligand HVEM in a cis manner on the surface of the same immune cell to maintain immune tolerance, while trans interactions on the surface of different immune cells mediate immunosuppressive effects. Dysregulation of the BTLA/HVEM axis can impair the functions of immune cells, particularly T lymphocytes, promoting immune escape of tumor cells and ultimately leading to tumor progression.
View Article and Find Full Text PDFCell Biochem Funct
January 2025
Department of Physiology and Pharmacology, Anhui University of Chinese Medicine, Hefei, Anhui, China.
The study of the mechanism of oligoasthenospermia, which is a major cause of male infertility, has been the focus of research in the field of male reproduction. TAp73, a member of the p53 family of oncogenes, is endowed with tumor-suppressing activity due to its structural and functional homology with p53. It has been found that TAp73, plays a key role in spermatogenesis and maintaining male reproduction.
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