Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues

Schwartz, Russell; Istrail, Sorin; King, Jonathan

doi:10.1110/ps.33201

Cited by 85 publications

(81 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Table 2 shows that, in contrast to VII, VIV is only slightly underrepresented respect to ADW and VIS. This result is indeed consistent with a previous study (24) showing that the frequency of stretches of three consecutive hydrophobic residues in general is the expected in proteins.…”

Section: Avoidance Of Amyloid Fibril Formation In Proteins: Amyloid Bsupporting

confidence: 93%

Sequence determinants of amyloid fibril formation

Paz

Serrano²

2003

Proc. Natl. Acad. Sci. U.S.A.

375

362

View full text Add to dashboard Cite

The establishment of rules that link sequence and amyloid feature is critical for our understanding of misfolding diseases. To this end, we have performed a saturation mutagenesis analysis on the de novodesigned amyloid peptide STVIIE (1). The positional scanning mutagenesis has revealed that there is a position dependence on mutation of amyloid fibril formation and that both very tolerant and restrictive positions to mutation can be found within an amyloid sequence. In this system, mutations that accelerate ␤-sheet polymerization do not always lead to an increase of amyloid products. On the contrary, abundant fibrils are typically found for mutants that polymerize slowly. From these experiments, we have extracted a sequence pattern to identify amyloidogenic stretches in proteins. The pattern has been validated experimentally. In silico sequence scanning of amyloid proteins also supports the pattern. Analysis of protein databases has shown that highly amyloidogenic sequences matching the pattern are less frequent in proteins than innocuous amino acid combinations and that, if present, they are surrounded by amino acids that disrupt their aggregating capability (amyloid breakers). This study provides the potential for a proteome-wide scanning to detect fibril-forming regions in proteins, from which molecules can be designed to prevent and͞or disrupt this process.I t is accepted that misfolding of peptides and proteins cause the fibrillar aggregates that characterize the group of diseases known as amyloidoses (1, 2). Despite active research, a detailed understanding of the molecular principles underlying the transformation of soluble proteins into amyloid aggregates is still lacking (1-3).The group of peptides and proteins capable of forming amyloid fibrils is very diverse (4-8). This group does not only consist of proteins involved in amyloid deposits in vivo (4), but also of nonpathogenic (15, 16) and designed peptides and proteins (7,8). X-ray fiber diffraction data indicate that all amyloid fibrils share a cross-␤-structure, regardless of the sequence or native fold of the soluble precursor (1, 2). Thus, an increasingly adopted view is that the ability to form amyloid fibrils is a general property of the polypeptide backbone (6). Nevertheless, the propensity of a given polypeptide to form amyloid fibrils depends enormously on amino acid composition (7-10).A protein has to be partially or fully unfolded to aggregate (1, 2). Yet, mutations leading to aggregation can alter (9, 10), or not alter (11, 12), protein stability. Aggregation from some peptides and proteins involved in relevant amyloidoses, such as type II diabetes and Alzheimer's and Parkinson's disease, does not require, however, previous unfolding, because these molecules are largely unstructured under physiological conditions (2). Nevertheless, most of the natively unfolded proteins in vivo do not undergo aggregation (13), indicating that unfolding is necessary, but not sufficient, to promote aggregation. Hence, there must be some sequence motifs tha...

show abstract

Section: Avoidance Of Amyloid Fibril Formation In Proteins: Amyloid Bsupporting

confidence: 93%

Sequence determinants of amyloid fibril formation

Paz

Serrano²

2003

Proc. Natl. Acad. Sci. U.S.A.

375

362

View full text Add to dashboard Cite

show abstract

“…More than 30 distinct positions were chosen for substitutions. Combinations of the individual mutations were designed based on the following guiding principles: 1) avoiding introduction of large clusters of charge or hydrophobicity to avoid destabilizing the IgG fold and to minimize binding to solvent ions; 31 2) incorporating diversity into the types of interactions, i.e ., not just enhancing electrostatic or hydrophobic contacts; and 3) dispersing mutations across the CH2 and CH3 domains. Based on these considerations, more than 150 unique mutant combinations were designed and experimentally evaluated.…”

Section: Resultsmentioning

confidence: 99%

Extending human IgG half-life using structure-guided design

Booth

Ramakrishnan

Narayan

et al. 2018

mAbs

View full text Add to dashboard Cite

Engineering of antibodies for improved pharmacokinetics through enhanced binding to the neonatal Fc receptor (FcRn) has been demonstrated in transgenic mice, non-human primates and humans. Traditionally, such approaches have largely relied on random mutagenesis and display formats, which fail to address related critical attributes of the antibody, such as effector functions or biophysical stability. We have developed a structure- and network-based framework to interrogate the engagement of IgG with multiple Fc receptors (FcRn, C1q, TRIM21, FcγRI, FcγRIIa/b, FcγRIIIa) simultaneously. Using this framework, we identified features that govern Fc-FcRn interactions and identified multiple distinct pathways for enhancing FcRn binding in a pH-specific manner. Network analysis provided a novel lens to study the allosteric impact of half-life-enhancing Fc mutations on FcγR engagement, which occurs distal to the FcRn binding site. Applying these principles, we engineered a panel of unique Fc variants that enhance FcRn binding while maintaining robust biophysical properties and wild type-like binding to activating receptors. An antibody harboring representative Fc designs demonstrates a half-life improvement of > 9 fold in transgenic mice and > 3.5 fold in cynomolgus monkeys, and maintains robust effector functions such as antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity.

show abstract

“…This is slightly different from the case of nCA-GFP where the very hydrophobic peptide is being translated and released from the ribosome first, leading to a very different sampling of folding states as it is being translated. The grouping of long stretches of hydrophobic residues has been shown to lead to an increase in aggregation, 27 which could lead to very different folding intermediates being sampled than the native GFP. This type of behavior has been harnessed to use GFP as a folding reporter.…”

Section: Discussionmentioning

confidence: 99%

Structural basis of fluorescence quenching in caspase activatable‐GFP

Nicholls

Hardy

2013

Protein Science

View full text Add to dashboard Cite

Apoptosis is critical for organismal homeostasis and a wide variety of diseases. Caspases are the ultimate executors of the apoptotic programmed cell death pathway. As caspases play such a central role in apoptosis, there is significant demand for technologies to monitor caspase function. We recently developed a caspase activatable-GFP (CA-GFP) reporter. CA-GFP is unique due to its ''dark'' state, where chromophore maturation of the GFP is inhibited by the presence of a C-terminal peptide. Here we show that chromophore maturation is prevented because CA-GFP does not fold into the robust b-barrel of GFP until the peptide has been cleaved by active caspase. Both CA-GFP and GFP 1-10 , a split form of GFP lacking the 11th strand, have similar secondary structure, different from mature GFP. A similar susceptibility to proteolytic digestion indicates that this shared structure is not the robust, fully formed GFP b-barrel. We have developed a model that suggests that as CA-GFP is translated in vivo it follows the same folding path as wild-type GFP; however, the presence of the appended peptide does not allow CA-GFP to form the barrel of the fully matured GFP. CA-GFP is therefore held in a ''pro-folding'' intermediate state until the peptide is released, allowing it to continue folding into the mature barrel geometry. This new understanding of the structural basis of the dark state of the CA-GFP reporter will enable manipulation of this mechanism in the development of reporter systems for any number of cellular processes involving proteases and potentially other enzymes.

show abstract

Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues

Cited by 85 publications

References 30 publications

Sequence determinants of amyloid fibril formation

Sequence determinants of amyloid fibril formation

Extending human IgG half-life using structure-guided design

Structural basis of fluorescence quenching in caspase activatable‐GFP

Contact Info

Product

Resources

About