IPC 2.0: prediction of isoelectric point and p<i>K</i>a dissociation constants

Kozłowski, Łukasz P.

doi:10.1093/nar/gkab295

Cited by 80 publications

(81 citation statements)

References 45 publications

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“…The isoelectric points (pIs) of a series of recombinant LOXL2s were determined by isoelectric focusing polyacrylamide gel electrophoresis (IEF-PAGE) (Table 2). The experimentally determined pIs are in good agreement with values predicted by Isoelectric Compute pI/MW [35] and Point Calculator 2.0 [36]. A slight smearing of fl-LOXL2 was detected and two major spots gave a pI of 5.5-5.9.…”

Section: The Isoelectric Point (Pi) Of Loxl2supporting

confidence: 82%

“…LOXL2 has been shown to oxidatively deaminate Lys residue(s) of the extracellular domain of PDGFRβ to an aldehyde [ 6 ]. The pI value of the extracellular domain of PDGFRβ is predicted to be 4.83 and 4.71 by Isoelectric Compute pI/MW [ 35 ] and Point Calculator 2.0 [ 36 ], respectively. It is possible that the interaction of LOXL2 and PDGFRβ is facilitated by the SRCR2 domain.…”

Section: Discussionmentioning

confidence: 99%

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Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2

et al. 2021

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Lysyl oxidase-like 2 (LOXL2) has emerged as a promising therapeutic target against metastatic/invasive tumors and organ and tissue fibrosis. LOXL2 catalyzes the oxidative deamination of lysine and hydroxylysine residues in extracellular matrix (ECM) proteins to promote crosslinking of these proteins, and thereby plays a major role in ECM remodeling. LOXL2 secretes as 100-kDa full-length protein (fl-LOXL2) and then undergoes proteolytic cleavage of the first two scavenger receptor cysteine-rich (SRCR) domains to yield 60-kDa protein (Δ1-2SRCR-LOXL2). This processing does not affect the amine oxidase activity of LOXL2 in vitro. However, the physiological importance of this cleavage still remains elusive. In this study, we focused on characterization of biophysical properties of fl- and Δ1-2SRCR-LOXL2s (e.g., oligomeric states, molecular weights, and hydrodynamic radii in solution) to gain insight into the structural role of the first two SRCR domains. Our study reveals that fl-LOXL2 exists predominantly as monomer but also dimer to the lesser extent when its concentration is <~1 mM. The hydrodynamic radius (Rh) determined by multi-angle light scattering coupled with size exclusion chromatography (SEC-MALS) indicates that fl-LOXL2 is a moderately asymmetric protein. In contrast, Δ1-2SRCR-LOXL2 exists solely as monomer and its Rh is in good agreement with the predicted value. The Rh values calculated from a 3D modeled structure of fl-LOXL2 and the crystal structure of the precursor Δ1-2SRCR-LOXL2 are within a reasonable margin of error of the values determined by SEC-MALS for fl- and Δ1-2SRCR-LOXL2s in mature forms in this study. Based on superimposition of the 3D model and the crystal structure of Δ1-2SRCR-LOXL2 (PDB:5ZE3), we propose a configuration of fl-LOXL2 that explains the difference observed in Rh between fl- and Δ1-2SRCR-LOXL2s in solution.

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Section: The Isoelectric Point (Pi) Of Loxl2supporting

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2

et al. 2021

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“…The protein characteristics, including the isoelectric point, lengths, and molecular weight of TaPIN proteins, were evaluated using the isoelectric point calculator [ 93 , 94 ] and ExPASy ( accessed on 12 May 2021). Subcellular localization was predicted using CELLO ( accessed on 12 May 2021).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions in Triticum aestivum L.

Kumar

Kherawat

Dey

et al. 2021

IJMS

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PIN-FORMED (PIN) genes play a crucial role in regulating polar auxin distribution in diverse developmental processes, including tropic responses, embryogenesis, tissue differentiation, and organogenesis. However, the role of PIN-mediated auxin transport in various plant species is poorly understood. Currently, no information is available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the PIN gene family in wheat to understand the evolution of PIN-mediated auxin transport and its role in various developmental processes and under different biotic and abiotic stress conditions. In this study, we performed genome-wide analysis of the PIN gene family in common wheat and identified 44 TaPIN genes through a homology search, further characterizing them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses led to the classification of TaPIN genes into seven different groups, providing evidence of an evolutionary relationship with Arabidopsis thaliana and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, transmembrane domains, and three-dimensional (3D) structure were also examined using various computational approaches. Cis-elements analysis of TaPIN genes showed that TaPIN promoters consist of phytohormone, plant growth and development, and stress-related cis-elements. In addition, expression profile analysis also revealed that the expression patterns of the TaPIN genes were different in different tissues and developmental stages. Several members of the TaPIN family were induced during biotic and abiotic stress. Moreover, the expression patterns of TaPIN genes were verified by qRT-PCR. The qRT-PCR results also show a similar expression with slight variation. Therefore, the outcome of this study provides basic genomic information on the expression of the TaPIN gene family and will pave the way for dissecting the precise role of TaPINs in plant developmental processes and different stress conditions.

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“…14 In the context of the full-length SSB protein, the absence of the electrostatic charges in the C-terminal tail of this mutant results in an increase in pI of this region from 3.9 ± 0.5 to 6.2 ± 0.5 and for the entire protein, 5.41 ± 0.09 to 8.95 ± 0.10. 91 The effect of the loss of 67% of the electrostatic charges in the tail region is the binding of the linker to the SSB OB-fold, thus explaining the four-fold increase in the intrinsic site size of the protein.…”

Section: The Acidic Tip Can Bind To Interactome Partnersmentioning

confidence: 99%

The mechanism of action of the SSB interactome reveals it is the first OB‐fold family of genome guardians in prokaryotes

Bianco

2021

Protein Science

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The single‐stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism in bacteria. This protein performs two distinct, but closely intertwined and indispensable functions in the cell. SSB binds to single‐stranded DNA (ssDNA) and at least 20 partner proteins resulting in their regulation. These partners comprise a family of genome guardians known as the SSB interactome. Essential to interactome regulation is the linker/OB‐fold network of interactions. This network of interactions forms when one or more PXXP motifs in the linker of SSB bind to an OB‐fold in a partner, with interactome members involved in competitive binding between the linker and ssDNA to their OB‐fold. Consequently, when linker‐binding occurs to an OB‐fold in an interactome partner, proteins are loaded onto the DNA. When linker/OB‐fold interactions occur between SSB tetramers, cooperative ssDNA‐binding results, producing a multi‐tetrameric complex that rapidly protects the ssDNA. Within this SSB‐ssDNA complex, there is an extensive and dynamic network of linker/OB‐fold interactions that involves multiple tetramers bound contiguously along the ssDNA lattice. The dynamic behavior of these tetramers which includes binding mode changes, sliding as well as DNA wrapping/unwrapping events, are likely coupled to the formation and disruption of linker/OB‐fold interactions. This behavior is essential to facilitating downstream DNA processing events. As OB‐folds are critical to the essence of the linker/OB‐fold network of interactions, and they are found in multiple interactome partners, the SSB interactome is classified as the first family of prokaryotic, oligosaccharide/oligonucleotide binding fold (OB‐fold) genome guardians.

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IPC 2.0: prediction of isoelectric point and pKa dissociation constants

Cited by 80 publications

References 45 publications

Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2

Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2

Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions in Triticum aestivum L.

The mechanism of action of the SSB interactome reveals it is the first OB‐fold family of genome guardians in prokaryotes

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