Effect of low-complexity regions on protein structure determination

Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation

The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.

Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation

The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.

Glycogen Synthase Kinase-3 Isoform Variants and Their Inhibitory Phosphorylation in Human Testes and Spermatozoa

PURPOSE

To clarify (phospho-) glycogen synthase kinase-3 (GSK3) isoform variants in the germline and soma of human testes and spermatozoa.

MATERIALS AND METHODS

GSK3 isoform variants in normospermatogenic and Sertoli cell-only (SCO) testicular biopsies and spermatozoa were examined.

RESULTS

In normospermatogenic testes, GSK3α and GSK3β variants 1 and 2 different in low complexity region (LCR) were expressed and their levels were decreased in SCO testes. GSK3β variant 3 was only expressed in SCO testes. GSK3β as well as GSK3α, the dominant isoforms in testes were decreased in SCO testes. In normospermatogenic testes, GSK3β were found in spermatogonia and markedly decreased in meiotic germ cells in which GSK3α was dominant. p-GSK3α/β were marginal in spermatogonia and early spermatocytes. In SCO testes, GSK3α/β immunoreactivity in seminiferous epithelia was weaker than those of normospermatogenic testes whereas p-GSK3α/β(Ser) immunoreactivity was visibly increased in Sertoli cells. GSK3α was dominant in ejaculated spermatozoa in which GSK3α and p-GSK3α(Ser) were found in the head, midpiece, and tail. In acrosome-reacted spermatozoa, GSK3α was found in the equatorial region of head, midpiece, and tail, and p-GSK3α(Ser) was only found in midpiece. During sperm capacitation, p-GSK3α(Ser) was significantly increased together with phosphotyrosine proteins and motility.

CONCLUSIONS

In human male germ cells, GSK3 isoforms different in LCRs switch from GSK3β to GSK3α during meiotic entry, suggesting the isoform-specific roles of GSK3α and GSK3β in meiosis and stemness or proliferation of spermatogonia, respectively. In dormant Sertoli cells of SCO testes kinase activity of GSK3 might be downregulated via inhibitory phosphorylation. In spermatozoa, inhibitory phosphorylation of GSK3α might be coupled with activation of motility during capacitation.

Understanding and identifying amino acid repeats

Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats.

Low complexity and disordered regions of proteins have different structural and amino acid preferences

Low complexity regions (LCRs) or non-random regions of a few amino acids are abundantly present in proteins. LCRs are traditionally considered as floppy structures with high solvent accessibility. Thus little attention was paid to them for structural studies. However LCRs have been found to contain information relevant to protein structure and various important functions. The present study is an attempt to understand the structural trend of LCRs. Here we report a study conducted to understand the structural trend, solvent accessibility and amino acid preferences of LCRs. The results show that LCRs might attain any type of secondary structure; however, the helix is frequently seen, whereas sheets occur rarely. We also found that LCRs are not always exposed on the surface. We found insignificant contribution of trans-membrane helices to the overall helix content. The LCRs having a secondary structure have different enrichment and depletion of amino acids from LCRs without a secondary structure and disordered protein sequences. However, LCRs of NMR structures showed compositional and functional similarity to the disordered regions of proteins. We also noted that in ∼3/4 LCRs, the entire amino acid did not have a single structural class, but rather an ensemble of more than one secondary structure, which indicates that they are found at places where structure transition occurs. Overall analysis suggests that the overall protein sequence has a greater influence on the structural and sequence enrichment rather than only the local amino acid composition of LCRs.

The first missense mutation of NHS gene in a Tunisian family with clinical features of NHS syndrome including cardiac anomaly

Nance-Horan Syndrome (NHS) or X-linked cataract-dental syndrome is a disease of unknown gene action mechanism, characterized by congenital cataract, dental anomalies, dysmorphic features and, in some cases, mental retardation. We performed linkage analysis in a Tunisian family with NHS in which affected males and obligate carrier female share a common haplotype in the Xp22.32-p11.21 region that contains the NHS gene. Direct sequencing of NHS coding exons and flanking intronic sequences allowed us to identify the first missense mutation (P551S) and a reported SNP-polymorphism (L1319F) in exon 6, a reported UTR-SNP (c.7422 C>T) and a novel one (c.8239 T>A) in exon 8. Both variations P551S and c.8239 T>A segregate with NHS phenotype in this family. Although truncations, frame-shift and copy number variants have been reported in this gene, no missense mutations have been found to segregate previously. This is the first report of a missense NHS mutation causing NHS phenotype (including cardiac defects). We hypothesize also that the non-reported UTR-SNP of the exon 8 (3'-UTR) is specific to the Tunisian population.

Low-complexity sequences and single amino acid repeats: not just "junk" peptide sequences

For decades proteins were thought to interact in a "lock and key" system, which led to the definition of a paradigm linking stable three-dimensional structure to biological function. As a consequence, any non-structured peptide was considered to be nonfunctional and to evolve neutrally. Surprisingly, the most commonly shared peptides between eukaryotic proteomes are low-complexity sequences that in most conditions do not present a stable three-dimensional structure. However, because these sequences evolve rapidly and because the size variation of a few of them can have deleterious effects, low-complexity sequences have been suggested to be the target of selection. Here we review evidence that supports the idea that these simple sequences should not be considered just "junk" peptides and that selection drives the evolution of many of them.

Structural biology of TRP channels

Structural studies on TRP channels, while limited, are poised for a quickened pace and rapid expansion. As of yet, no high-resolution structure of a full length TRP channel exists, but low-resolution electron cryomicroscopy structures have been obtained for 4 TRP channels, and high-resolution NMR and X-ray crystal structures have been obtained for the cytoplasmic domains, including an atypical protein kinase domain, ankyrin repeats, coiled coil domains and a Ca(2+)-binding domain, of 6 TRP channels. These structures enhance our understanding of TRP channel assembly and regulation. Continued technical advances in structural approaches promise a bright outlook for TRP channel structural biology.

A software tool to accelerate design of protein constructs for recombinant expression

Structural and biochemical analysis of proteins requires access to purified protein material. Modern molecular biology technologies facilitate straightforward molecular cloning and expression analysis of multiple protein constructs in parallel, and such approaches have proven very efficient to identify samples suitable for further analysis. A variety of information can be used to support rational design of protein constructs. This includes, e.g. prediction of secondary structure elements, protein domain predictions, and structure prediction methods such as threading. To fully access the available information, collation of data extracted from several different sources is required. This can be cumbersome and sometimes also confusing due to for example different implementation of amino acid residue numbering schemes. The SGC Domain Boundary Analyser tool provides a graphical interface that simplifies and accelerates rational design of protein expression constructs.

Genome-wide evidence for selection acting on single amino acid repeats

Low complexity and homopolymer sequences within coding regions are known to evolve rapidly. While their expansion may be deleterious, there is increasing evidence for a functional role associated with these amino acid sequences. Homopolymer sequences are thought to evolve mostly through replication slippage and, therefore, they may be expected to be longer in regions with relaxed selective constraint. Within the coding sequences of eukaryotes, alternatively spliced exons are known to evolve under relaxed constraints in comparison to those exons that are constitutively spliced because they are not included in all of the mature mRNA of a gene. This relaxed exposure to selection leads to faster rates of evolution for alternatively spliced exons in comparison to constitutively spliced exons. Here, we have tested the effect of splicing on the structure (composition, length) of homopolymer sequences in relation to the splicing pattern in which they are found. We observed a significant relationship between alternative splicing and homopolymer sequences with alternatively spliced genes being enriched in number and length of homopolymer sequences. We also observed lower codon diversity and longer homocodons, suggesting a balance between slippage and point mutations linked to the constraints imposed by selection.

The Center for Eukaryotic Structural Genomics

The Center for Eukaryotic Structural Genomics (CESG) is a "specialized" or "technology development" center supported by the Protein Structure Initiative (PSI). CESG's mission is to develop improved methods for the high-throughput solution of structures from eukaryotic proteins, with a very strong weighting toward human proteins of biomedical relevance. During the first three years of PSI-2, CESG selected targets representing 601 proteins from Homo sapiens, 33 from mouse, 10 from rat, 139 from Galdieria sulphuraria, 35 from Arabidopsis thaliana, 96 from Cyanidioschyzon merolae, 80 from Plasmodium falciparum, 24 from yeast, and about 25 from other eukaryotes. Notably, 30% of all structures of human proteins solved by the PSI Centers were determined at CESG. Whereas eukaryotic proteins generally are considered to be much more challenging targets than prokaryotic proteins, the technology now in place at CESG yields success rates that are comparable to those of the large production centers that work primarily on prokaryotic proteins. We describe here the technological innovations that underlie CESG's platforms for bioinformatics and laboratory information management, target selection, protein production, and structure determination by X-ray crystallography or NMR spectroscopy.