Exploring the relationships between protein sequence, structure and solubility

Trainor, Kyle; Broom, Aron; Meiering, Elizabeth M.

doi:10.1016/j.sbi.2017.01.004

Cited by 66 publications

(59 citation statements)

References 68 publications

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“…The three repeat regions of the FapC sequence are highly conserved among pseudomonads, and therefore, we hypothesized that these regions are critical for the macromolecular assembly of amyloid fibrils. A variety of bioinformatics tools has been developed to predict aggregation propensity and solubility of proteins [21], and we applied two of these algorithms to examine the repeat sequences of FapC from P. aeruginosa PAO1 (Fig. 2a, b).…”

Section: Resultsmentioning

confidence: 99%

Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms

Bleem

Christiansen

Madsen

et al. 2018

Journal of Molecular Biology

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Amyloids are typically associated with neurodegenerative diseases, but recent research demonstrates that several bacteria utilize functional amyloid fibrils to fortify the biofilm extracellular matrix and thereby resist antibiotic treatments. In Pseudomonas aeruginosa, these fibrils are composed predominantly of FapC, a protein with high-sequence conservation among the genera. Previous studies established FapC as the major amyloid subunit, but its mechanism of fibril formation in P. aeruginosa remained largely unexplored. Here, we examine the FapC sequence in greater detail through a combination of bioinformatics and protein engineering, and we identify specific motifs that are implicated in amyloid formation. Sequence regions of high evolutionary conservation tend to coincide with regions of high amyloid propensity, and mutation of amyloidogenic motifs to a designed, non-amyloidogenic motif suppresses fibril formation in a pH-dependent manner. We establish the particular significance of the third repeat motif in promoting fibril formation and also demonstrate emergence of soluble oligomer species early in the aggregation pathway. The insights reported here expand our understanding of the mechanism of amyloid polymerization in P. aeruginosa, laying the foundation for development of new amyloid inhibitors to combat recalcitrant biofilm infections.

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Section: Resultsmentioning

confidence: 99%

Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms

Bleem

Christiansen

Madsen

et al. 2018

Journal of Molecular Biology

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“…Several algorithms are available to predict solubility of proteins. 73 Various factors in seminal fluid influence the solubility of SEVI precursors. For instance, a decrease in pH, if any, will increase solubility due to the increase in the number of positive charges.…”

Section: Increasing Solubility Of Sevi Precursors (Methods 6)mentioning

confidence: 99%

“…In these conditions, no enhancement of HIV viral activity is expected. Several algorithms are available to predict solubility of proteins . Various factors in seminal fluid influence the solubility of SEVI precursors.…”

Section: Inhibition Of Sevi‐enhanced Hiv Viral Infectionmentioning

confidence: 99%

Semen‐derived amyloidogenic peptides—Key players of HIV infection

Lee

Ramamoorthy

2018

Protein Science

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Misfolding and amyloid aggregation of intrinsically disordered proteins (IDPs) are implicated in a variety of diseases. Studies have shown that membrane plays important roles on the formation of intermediate structures of IDPs that can initiate (and/or speed-up) amyloid aggregation to form fibers. The process of amyloid aggregation also disrupts membrane to cause cell death in amyloid diseases like Alzheimer's disease and type-2 diabetes. On the other hand, recent studies reported the membrane fusion properties of amyloid fibers. Remarkably, amyloid-fibril formation by short peptide fragments of highly abundant prostatic acidic-phosphatase (PAP) in human semen and are capable of boosting the rate of HIV infection up to 400,000-fold during sexual contact. Unlike the least toxic fully matured fibers of most amyloid proteins, the semen-derived enhancer of virus infection (SEVI) amyloid-fibrils of PAP peptide fragments are highly potent in rendering the maximum rate of HIV infection. This unusual property of amyloid fibers has witnessed increasing number of studies on the biophysical aspects of fiber formation and fiber-membrane interactions. NMR studies have reported a highly disordered partial helical structure in a membrane environment for the intrinsically disordered PAP peptide that promotes the fusion of the viral membrane with that of host cells. The purpose of this review article is to unify and integrate biophysical and immunological research reported in the previous studies on SEVI. Specifically, amyloid aggregation, dramatic HIV infection enhancing properties, membrane fusion properties, high resolution NMR structure, and approaches to eliminate the enhancement of HIV infection of SEVI peptides are discussed.

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“…The amino acid sequence (primary structure) has effects on protein folding, modification, stability and solubility 27, 28, 29. Reports surrounding production of monoclonal antibodies (mAbs) suggest that unique sequence features influence the effectiveness of recombinant protein production 30, 31, 32.…”

mentioning

confidence: 99%

“…Reports surrounding production of monoclonal antibodies (mAbs) suggest that unique sequence features influence the effectiveness of recombinant protein production 30, 31, 32. For bacterial expression systems, computational tools have been implemented to predict of surface properties to allow rational design of recombinant targets with increased protein solubility of otherwise insoluble or poorly soluble target proteins 29, 33, 34, 35, 36. Previous work has established that charge and polarity influences protein solubility 37.…”

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confidence: 99%

A protein chimera strategy supports production of a model “difficult‐to‐express” recombinant target

et al. 2018

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Due in part to the needs of the biopharmaceutical industry, there has been an increased drive to generate high quality recombinant proteins in large amounts. However, achieving high yields can be a challenge as the novelty and increased complexity of new targets often makes them ‘difficult‐to‐express’. This study aimed to define the molecular features that restrict the production of a model ‘difficult‐to‐express’ recombinant protein, Tissue Inhibitor Metalloproteinase‐3 (TIMP‐3). Building from experimental data, computational approaches were used to rationalize the redesign of this recombinant target to generate a chimera with enhanced secretion. The results highlight the importance of early identification of unfavourable sequence attributes, enabling the generation of engineered protein forms that bypass ‘secretory’ bottlenecks and result in efficient recombinant protein production.

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Exploring the relationships between protein sequence, structure and solubility

Cited by 66 publications

References 68 publications

Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms

Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms

Semen‐derived amyloidogenic peptides—Key players of HIV infection

A protein chimera strategy supports production of a model “difficult‐to‐express” recombinant target

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