The Nedd4-1 WW Domain Recognizes the PY Motif Peptide through Coupled Folding and Binding Equilibria.

The four WW domains of human Nedd4-1 (neuronal precursor cell expressed developmentally downregulated gene 4-1) interact with the PPxY (PY) motifs of the human epithelial Na(+) channel (hENaC) subunits, with the third WW domain (WW3*) showing the highest affinity. We have shown previously that the α-hENaC PY motif binding interface of WW3* undergoes conformational exchange on the millisecond time scale, indicating that conformational sampling plays a role in peptide recognition. To further understand this role, the structure and dynamics of hNedd4-1 WW3* were investigated. The nuclear Overhauser effect-derived structure of apo-WW3* resembles the domain in complex with the α-hENaC peptide, although particular side chain conformations change upon peptide binding, which was further investigated by molecular dynamics simulations. Model-free analysis of the (15)N nuclear magnetic resonance spin relaxation data showed that the apo and peptide-bound states of WW3* have similar backbone picosecond to nanosecond time scale dynamics. However, apo-WW3* exhibits pronounced chemical exchange on the millisecond time scale that is quenched upon peptide binding. (1)HN and (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments at various temperatures revealed that apo-WW3* exists in an equilibrium between the natively folded peptide binding-competent state and a random coil-like denatured state. The thermodynamics of the folding equilibrium was determined by fitting a thermal denaturation profile monitored by circular dichroism spectroscopy in combination with the CPMG data, leading to the conclusion that the unfolded state is populated to ∼ 20% at 37 °C. These results show that the binding of the hNedd4-1 WW3* domain to α-hENaC is coupled to the folding equilibrium.

Chemical synthesis of a pore-forming antimicrobial protein, caenopore-5, by using native chemical ligation at a glu-cys site.

The 2014 report from the World Health Organization (WHO) on antimicrobial resistance revealed an alarming rise in antibiotic resistance all around the world. Unlike classical antibiotics, with the exception of a few species, no acquired resistance towards antimicrobial peptides (AMPs) has been reported. Therefore, AMPs represent leads for the development of novel antibiotics. Caenopore-5 is constitutively expressed in the intestine of the nematode Caenorhabditis elegans and is a pore-forming AMP. The protein (82 amino acids) was successfully synthesised by using Boc solid-phase peptide synthesis and native chemical ligation. No γ-linked by-product was observed despite the use of a C-terminal Glu-thioester. The folding of the synthetic protein was confirmed by (1) H NMR spectroscopy and circular dichroism and compared with data recorded for recombinant caenopore-5. The permeabilisation activities of the protein and of shortened analogues were evaluated.

Structure and dynamics of human Nedd4-1 WW3 in complex with the αENaC PY motif.

Nedd4-1 (neuronal precursor cell expressed developmentally downregulated gene 4-1) is an E3 ubiquitin ligase that interacts with and negatively regulates the epithelial Na(+) channel (ENaC). The WW domains of Nedd4-1 bind to the ENaC subunits via recognition of PY motifs. Human Nedd4-1 (hNedd4-1) contains four WW domains with the third domain (WW3*) showing the strongest affinity to the PY motif. To understand the mechanism underlying this binding affinity, we have carried out NMR structural and dynamics analyses of the hNedd4-1 WW3* domain in complex with a peptide comprising the C-terminal tail of the human ENaC α-subunit. The structure reveals that the peptide interacts in a similar manner to other WW domain-ENaC peptide structures. Crucial interactions that likely provide binding affinity are the broad XP groove facilitating additional contacts between the WW3* domain and the peptide, compared to similar complexes, and the large surface area buried (83Å(2)) between R430 (WW3*) and L647' (αENaC). This corroborates the model-free analysis of the (15)N backbone relaxation data, which showed that R430 is the most rigid residue in the domain (S(2)=0.90±0.01). Carr-Purcell-Meiboom-Gill relaxation dispersion analysis identified two different conformational exchange processes on the µs-ms time-scale. One of these processes involves residues located at the peptide binding interface, suggesting conformational exchange may play a role in peptide recognition. Thus, both structural and dynamic features of the complex appear to define the high binding affinity. The results should aid interpretation of biochemical data and modeling interfaces between Nedd4-1 and other interacting proteins.

MALDI-imaging enables direct observation of kinetic and thermodynamic products of mixed peptide fiber assembly.

Controlling the self-assembly of multicomponent systems provides a key to designing new materials and understanding the molecular complexity of biology. Here, we demonstrate the first use of MALDI-imaging to characterize a multicomponent self-assembling peptide fiber. Observations of mixed peptide systems over time demonstrate how simple sequence variation can change the balance between kinetic and thermodynamic products.

Synthesis and activity of a diselenide bond mimetic of the antimicrobial protein caenopore-5.

Antimicrobial proteins are a rich source of new lead compounds for the development of new drugs that will tackle global resistance towards existing antibiotics. Caenopore-5 (Cp-5) is an antimicrobial protein (AMP) expressed in the intestine of the nematode Caenorhabditis elegans and is a member of the lipid binding saposin-like-protein family, composed of 5 α-helices and 3 disulfide bonds. Substitution of the 7Cys and 81Cys by two selenocysteine 7U and 81U afforded a selenocysteine analogue [7Sec-81Sec]-Cp-5, which displayed a higher stability (using thermal circular dichroism) compared to the native protein Cp-5. [7Sec-81Sec]-Cp-5 and an N-terminal truncated peptide exhibited cell permeability similar to the wild type Cp-5.

Controlling gelation with sequence: Towards programmable peptide hydrogels.

UNLABELLED: The self-assembling peptide IKHLSVN, inspired by inspection of a protein-protein interface, has previously been reported as one of a new class of bio-inspired peptides. Here the peptide, dubbed littleSven, and modifications designed to probe the resilience of the sequence to self-assembly, is characterised. Although the parent peptide did not form a hydrogel, small modifications to the sequence (one side chain or an N-terminus modification) led to hydrogels with properties (eg. gelation time and rheology) that could be tuned by these small alterations. The results suggest that peptides derived from protein-protein interfaces are resilient to changes in sequence and can be harnessed to form hydrogels with controlled properties. STATEMENT OF SIGNIFICANCE: Natural occurring self-assembly peptides are attractive building blocks for engineered bionanomaterials due to their biocompatibility and biodegradability. The bio-inspired self-assembly peptide, IKHLSVN, was used as a template to design peptides that readily formed hydrogels. The peptide sequence was specifically tuned to create a bionanomaterial with different properties that could be exploited downstream for a broad range of applications: nanowires, drug release, vaccine adjuvant, tissue engineering. We describe how small modifications to the parent peptide alter the amyloid-like characteristics and gel strength for each peptide.