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Helical peptides, as well as proteins composed of helical peptides, play essential roles in various biological processes, including their functions as components of cell membranes and their interactions with biological membranes. Therefore, it is crucial to predict the propensity and structural characteristics of helices formed in solution or lipid environments for specific peptide sequences. Melittin and pexiganan are antimicrobial peptides (AMPs) that possess distinct sequence characteristics but exhibit similar structural properties in both solution and lipid environments. In this study, we conducted molecular dynamics simulations to investigate how the presence of counter ions creates differences in structural characteristics between these two peptides in solution. By analyzing the structures formed for each AMP using extended helical projections, we aimed to uncover the underlying principles governing the interaction between counter ions and peptide sequences, leading to the formation of stable structures. It was found that the coordination of counter ions effectively extends the helical surface and stabilizes the extended helix by reducing the electrostatic repulsion between charged residues. Our results demonstrate how sequence specificity influences helical structure formation in solution and provide an explanation for the varying degrees of synergistic effects exhibited by different helical AMPs. [ABSTRACT FROM AUTHOR]

[Display omitted] Precise control of molecular arrangement is essential for functional molecular assemblies. A linear (I-shaped) amphiphilic block copolypeptide, polysarcosine- b -(l -Leu-Aib) 6 (I-SL12), which has a hydrophilic polysarcosine (PSar) chain and a hydrophobic helical block, was reported to self-assemble into nanotubes by regular packing of the Leu side chains. Here, we have synthesized a T-shaped amphiphilic block copolypeptide, (l -Leu-Aib) 3 -AzF(PSar)-Aib-(l -Leu-Aib) 2 (T-SL12), to investigate the effect of molecular geometry on the morphology of molecular assemblies. Unlike conventional I-SL12, T-SL12 self-assembles into helical nanotubes. A mixture of T-SL12 (a right-handed helix) and polysarcosine- b -(d -Leu-Aib) 6 (I-SdL12, a left-handed helix) formed flat rod-shaped structures, while the mixture of T-SL12 and I-SL12 (both right-handed) forms nanotubes with an 80-nm diameter. This result indicates that stereo-complexes was formed between T-SL12 and I-SdL12. Peptidic flat-rod were obtained at ratios of T-SL12 and I-SdL12 from 1:1 to 1:3 (wt/wt), although their width (ca. 12 nm) and length (50–200 nm) did not change with stoichiometry. The thickness (6 nm) of the flat rod was measured by AFM. From these dimensions, we propose that the minor axis of peptidic flat-rod is composed of two stereo-complexed heterodimers of T-SL12 and I-SdL12 by orienting the I-SdL12s facing each other, and that this four-peptide unit is repeated side-by-side along the long axis. [ABSTRACT FROM AUTHOR]

The global burden of the SARS-CoV-2 pandemic is thought to result from a high viral transmission rate. Here, we consider mechanisms that influence host cell–virus binding between the SARS-CoV-2 spike glycoprotein (SPG) and the human angiotensin-converting enzyme 2 (ACE2) with a series of peptides designed to mimic key ACE2 hot spots through adopting a helical conformation analogous to the N-terminal α1 helix of ACE2, the region experimentally shown to bind to the SARS-CoV-2 receptor-binding domain (RBD). The approach examines putative structure/function relations by assessing SPG binding affinity with surface plasmon resonance (SPR). A cyclic peptide (c[KFNHEAEDLFEKLM]) was characterized in an α-helical conformation with micromolar affinity (KD = 500 µM) to the SPG. Thus, stabilizing the helical structure of the 14-mer through cyclization improves binding to SPG by an order of magnitude. In addition, end-group peptide analog modifications and residue substitutions mediate SPG binding, with net charge playing an apparent role. Therefore, we surveyed reported viral variants, and a correlation of increased positive charge with increased virulence lends support to the hypothesis that charge is relevant to enhanced viral fusion. Overall, the structure/function relationship informs the importance of conformation and charge for virus-binding analog design. [ABSTRACT FROM AUTHOR]

Amide-linked homopolymers of sialic acid offer the advantages of stable secondary structure and increased bioavailability making them useful constructs for pharmaceutical design and drug delivery. Defining the structural characteristics that give rise to secondary structure in aqueous solution is challenging in homopolymeric material due to spectral overlap in NMR spectra. Having previously developed computational tools for heteroologomers with resolved spectra, we now report that application of these methods in combination with circular dichroism, NH/ND NMR exchange rates and nOe data has enabled the structural determination of a neutral, δ-amide-linked homopolymer of a sialic acid analogue called Neu2en. The results show that the inherent planarity of the pyranose ring in Neu2en brought about by the α,δ-conjugated amide bond serves as the primary driving force of the overall conformation of the homooligomer. This peptide surrogate has an excellent bioavailability profile, with half-life of ∼12 h in human blood serum, which offers a viable peptide scaffold that is resistant to proteolytic degradation. Furthermore, a proof-of-principle study illustrates that Neu2en oligomers are functionalizable with small molecule ligands using 1,3-dipolar cycloaddition chemistry.

The global burden of the SARS-CoV-2 pandemic is thought to result from a high viral transmission rate. Here, we consider mechanisms that influence host cell–virus binding between the SARS-CoV-2 spike glycoprotein (SPG) and the human angiotensin-converting enzyme 2 (ACE2) with a series of peptides designed to mimic key ACE2 hot spots through adopting a helical conformation analogous to the N-terminal α1 helix of ACE2, the region experimentally shown to bind to the SARS-CoV-2 receptor-binding domain (RBD). The approach examines putative structure/function relations by assessing SPG binding affinity with surface plasmon resonance (SPR). A cyclic peptide (c[KFNHEAEDLFEKLM]) was characterized in an α-helical conformation with micromolar affinity (KD = 500 µM) to the SPG. Thus, stabilizing the helical structure of the 14-mer through cyclization improves binding to SPG by an order of magnitude. In addition, end-group peptide analog modifications and residue substitutions mediate SPG binding, with net charge playing an apparent role. Therefore, we surveyed reported viral variants, and a correlation of increased positive charge with increased virulence lends support to the hypothesis that charge is relevant to enhanced viral fusion. Overall, the structure/function relationship informs the importance of conformation and charge for virus-binding analog design.

In Huntington's disease, the length of the polyglutamine tract in the mutant protein correlates positively with the formation of aggregates and disease symptoms and severity of the disease. Some disease‐modifying factors exist. However, no organized study has been carried out to investigate the effect of polyglutamine length in the mutant protein on the efficacy of a therapeutic strategy. We had shown earlier that the helical peptide arising out of the N‐terminal stretch of normal huntingtin is able to inhibit aggregation of a number of proteins, including luciferase, α‐synuclein, p53, and Rnq1. In this work, we show that polyglutamine stretches of differing lengths, namely 51Q, 72Q, and 103Q, form a mixture of aggregates at different rates, with the rate increasing in a polyQ length‐dependent manner. The helical peptide is able to inhibit the rate of aggregation. The extent of inhibition was different when measuring either total aggregation or only fibrillar aggregates, suggesting that the helical peptide with benign polyQ stretch alters the aggregation landscape of different elongated polyQ lengths differently. Our results suggest that designing a therapeutic approach to inhibit protein aggregation must take note of polyQ length of the protein. [ABSTRACT FROM AUTHOR]

Impaired macroautophagy/autophagy is involved in the pathogenesis of hepatic fibrosis. However, how aberrant autophagy promotes fibrosis is far from understood. Here, we aimed to define a previously unrevealed pro-fibrotic mechanism for the stress protein TRIB3 (tribbles pseudokinase 3)-mediated autophagy dysfunction. Human fibrotic liver tissues were obtained from patients with cirrhosis who underwent an open surgical repair process. The functional implications of TRIB3 were evaluated in mouse models of hepatic fibrosis induced by bile duct ligation (BDL) or thioacetamide (TAA) injection. Human fibrotic liver tissues expressed higher levels of TRIB3 and selective autophagic receptor SQSTM1/p62 (sequestosome 1) than nonfibrotic tissues and the elevated expression of TRIB3 and SQSTM1 was positively correlated in the fibrotic tissues. Silencing Trib3 protected against experimentally induced hepatic fibrosis, accompanied by restored autophagy activity in fibrotic liver tissues. Furthermore, TRIB3 interacted with SQSTM1 and hindered its binding to MAP1LC3/LC3, which caused the accumulation of SQSTM1 aggregates and obstructed autophagic flux. The TRIB3-mediated autophagy impairment not only suppressed autophagic degradation of late endosomes but also promoted hepatocellular secretion of INHBA/Activin A-enriched exosomes which caused migration, proliferation and activation of hepatic stellate cells (HSCs), the effector cells of liver fibrosis. Disrupting the TRIB3-SQSTM1 interaction with a specific helical peptide exerted potent protective effects against hepatic fibrosis by restoring autophagic flux in hepatocytes and HSCs. Together, stress-elevated TRIB3 expression promotes hepatic fibrosis by interacting with SQSTM1 and interfering with its functions in liver-parenchymal cells and activating HSCs. Targeting this interaction is a promising strategy for treating fibroproliferative liver diseases. Abbreviations: 3-MA: 3-methyladenine; AAV: adeno-associated virus; ACTA2/α-SMA: actin, alpha 2, smooth muscle, aorta; BDL: bile duct ligation; BECN1/Beclin 1: beclin 1, autophagy related; CHX: cycloheximide; CQ: chloroquine; Edu: 5-ethynyl-2-deoxyuridine; ESCRT: endosomal sorting complexes required for transport; HSC: hepatic stellate cell; ILV: intralumenal vesicle; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MVB: multivesicular body; PIK3C3: phosphatidylinositol 3-kinase, catalytic subunit type 3; PPI: protein-protein interaction; SQSTM1/p62: sequestosome 1; TAA: thioacetamide; TEM: transmission electron microscopy; TGFB1/TGFβ1: transforming growth factor, beta 1; TLR2: toll-like receptor 2; TRIB3: tribbles pseudokinase 3 [ABSTRACT FROM AUTHOR]

Biopolymer immobilization strategies, self‐assembly systems and adsorption phenomenon in general are crucial for the development of methods that work on the basis of the surface‐detection principle, including electrochemistry. A mechanistic view into the interaction of biopolymers with electrode surfaces is also important for studying fundamental and dynamic processes such as electron/proton transport. In this sense, the utilization of new approaches for investigating the interfacial behavior of immobilized biomolecular architectures is a permanent focus. Here we use a molecular dynamics (MD) approach to simulate the structural changes and metallic surface interactions of a model 21‐mer peptide of His (H) and Ala (A), A3(HA2)6, a peptidic proton wire (H‐wire). This H‐wire was previously proposed for the electrochemical study of proton transfer at mercury electrodes (Langmuir, 2018, 34, 6997). The rigid solid mercury mono‐atomic layer (α‐mercury lattice model) was used systematically in all our simulations. The calculations were performed in a simulation box with 1, 16 and 32 H‐wire strands attached covalently to the mercury layer via the thiol group of a cysteinamide residue appended to the H‐wire C‐terminus. The internal alpha‐helical configuration of H‐wires was maintained by the presence of 2,2,2‐trifluoroethanol. It was shown that both the surface density of H‐wires and the protonation state of His residues play a decisive role in the structural stability and orientation of the peptide to the surface, whereas the applied voltage only has a mild effect on it, especially in case of 16 and 32 H‐wire strand configurations. The MD simulations presented here could be used for the further investigation of other peptides at metallic surfaces and for electrochemical analyses of structural changes of surface‐attached peptides that depend on their protonation states and other external factors. [ABSTRACT FROM AUTHOR]

Transforming growth factor-β/bone morphogenetic protein (TGF-β/BMP) signaling plays a fundamental role in embryonic skeletal development and postnatal bone homeostasis. The signaling pivot protein BMP-2 belongs to the TGF-β superfamily and has been implicated in the pathogenesis of osteonecrosis of femoral head (ONFH). The biologically functional BMP-2 is a homodimer that has two tightly packed cores at its dimerization interface; each core is defined by the intermolecular interaction between a helical arm from one monomer and a hydrophobic pocket from another monomer. Inhibition and disruption of BMP-2 dimerization have been recognized as an attractive therapeutic strategy against ONFH. Here, we investigate the self-binding behavior of helical arm-derived peptides to the BMP-2 dimerization interface. The native BMP-2 helical arm and its several grafted versions from BMP-4, BMP-6 and BMP-7 are stripped from the intact dimerization interface to generate a number of isolated helical peptides. Computational simulations demonstrate that the stripping does not substantially influence the direct intermolecular interaction between BMP-2 monomer and these helical peptides or desolvation effect upon the interaction. However, the C-terminus of stripped peptides is found to have an intrinsic disorder and large flexibility in the isolated state, which would impair the rebinding of stripped peptides to BMP-2. Next, we rationally design a hydrocarbon bridge across the C-terminal residues 65 and 69 of helical peptides, which can effectively constrain peptide conformational flexibility in the isolated state, thus considerably promoting the binding potency of stripped helical peptides. Circular dichroism (CD) spectroscopy reveals that the peptide helicity increases from 51.8 to 67.9% upon hydrocarbon stapling. Fluorescence polarization assays substantiate that, as designed, the stapling can convert these helical peptides from weak binders to moderate or good binders of BMP-2 protein; their Kd values are improved by up to ~ fourfold. [ABSTRACT FROM AUTHOR]

Abstract: Modulation of the electronic band profiles of wide band gap GaN semiconductors is achieved by the macromolecular dipole potentials exerted from ordered monolayers of synthetic, nonbiological aldehyde terminated helical peptides deposited on wet chemically oxidized GaN surfaces functionalized with aminosilanes. The selective coupling of either N‐ or C‐terminal to the amino‐terminated surface enables one to control the direction of the dipole moment, while the number of amino acids determines its magnitude. After confirming the formation of highly ordered peptide monolayers, the impact of macromolecular dipole potentials is quantified by electrochemical impedance spectroscopy. Moreover, the chronoamperometry measurements of ferrocene‐terminated peptides suggest that the transfer of electrons injected from ferrocene follows inelastic hopping, while the current responses of peptides with no ferrocene moieties are purely capacitive. Finally, the same functionalization steps are transferred to GaN/AlGaN/GaN high electron mobility transistor structures. Stable and quantitative modulation of the current–voltage characteristics of the 2D electron gas by the deposition of bioinspired peptides is a promising strategy for the macromolecular dipole engineering of GaN semiconductors. [ABSTRACT FROM AUTHOR]

[Display omitted] • An engineered peptide zp80r showed bioactivity against all ESKAPE strains. • d -arginine substitution increased proteolytic stability of the synthetic peptide. • Peptide zp80r suppressed growth of persisters and cellular swarming. • Peptide zp80r inhibited bacterial contamination in chilled fresh pork. The co-existence of various pathogenic bacteria on the surface of pork products exacerbates difficulties in food safety control. Developing broad-spectrum and stable antibacterial agents that are not antibiotics is an unmet need. To address this issue, all l -arginine residues of a reported peptide (IIRR) 4 -NH 2 (zp80) were substituted with the corresponding D enantiomers. This novel peptide (IIrr) 4 -NH 2 (zp80r) was expected to maintain favourable bioactivity against ESKAPE strains and have enhanced proteolytic stability compared with zp80. In a series of experiments, zp80r maintained favourable bioactivities against starvation-induced persisters. Electron microscopy and fluorescent dye assays were used to verify the antibacterial mechanism of zp80r. Importantly, zp80r reduced bacterial colonies in chilled fresh pork contaminated with multiple bacterial species. This newly designed peptide is a potential antibacterial candidate to combat problematic foodborne pathogens during storage of pork. [ABSTRACT FROM AUTHOR]

Lysine-based amphipathic nonapeptides, including homochiral peptides [Ac-( l -Lys- l -Lys-Xaa) 3 -NH 2 (Xaa = Gly, Ala, Aib, Ac 5 c, or Ac 6 c) and Ac-( d -Lys- d -Lys-Aib) 3 -NH 2 ], a heterochiral peptide [Ac-( l -Lys- d -Lys-Aib) 3 -NH 2 ], and a racemic mixture of diastereomeric peptides [Ac-( rac -Lys- rac -Lys-Aib) 3 -NH 2 ] were designed and synthesized to investigate the relationship between their preferred secondary structures and their antimicrobial activity. Peptide 5 , [Ac-( l -Lys- l -Lys-Ac 6 c) 3 -NH 2 ] formed a stable α-helical structure and exhibited strong activity against Gram-negative bacteria ( Escherichia coli and Pseudomonas aeruginosa ). [ABSTRACT FROM AUTHOR]

[Display omitted] The Wnt/β-catenin signaling pathway causes transcriptional activation through the interaction between β-catenin and T cell-specific transcription factor (TCF) and regulates a wide variety of cellular responses, including proliferation, differentiation and cell motility. Excessive transcriptional activation of the Wnt/β-catenin pathway is implicated in developing or exacerbating various cancers. We have recently reported that liver receptor homolog-1 (LRH-1)-derived peptides inhibit the β-catenin/TCF interaction. In addition, we developed a cell-penetrating peptide (CPP)-conjugated LRH-1-derived peptide that inhibits the growth of colon cancer cells and specifically inhibits the Wnt/β-catenin pathway. Nonetheless, the inhibitory activity of the CPP-conjugated LRH-1-derived peptide was unsatisfactory (ca. 20 μM), and improving the bioactivity of peptide inhibitors is required for their in vivo applications. In this study, we optimized the LRH-1-derived peptide using in silico design to enhance its activity further. The newly designed peptides showed binding affinity toward β-catenin comparable to the parent peptide. In addition, the CPP-conjugated stapled peptide, Penetratin-st6 , showed excellent inhibition (ca. 5 μM). Thus, the combination of in silico design by MOE and MD calculations has revealed that logical molecular design of PPI inhibitory peptides targeting β-catenin is possible. This method can be also applied to the rational design of peptide-based inhibitors targeting other proteins. [ABSTRACT FROM AUTHOR]

A peptide-based protein knockdown system for inducing nuclear receptors degradation via the ubiquitin–proteasome system was developed. Specifically, the designed molecules were composed of two biologically active scaffolds: a peptide that binds to the estrogen receptor α (ERα) surface and an MV1 molecule that binds to cellular inhibitors of apoptosis proteins (IAP: cIAP1/cIAP2/XIAP) to induce ubiquitylation of the ERα. The hybrid peptides induced IAP-mediated ubiquitylation followed by proteasomal degradation of the ERα. Those peptides were also applicable for inducing androgen receptor (AR) degradation. [ABSTRACT FROM AUTHOR]

A five-membered ring amino acid (Ac 5 c), the peptides of which exhibit a preference for helical secondary structures, was introduced into peptides for the purpose of designing coiled coil peptides with high binding affinities. We prepared five types of peptides containing Ac 5 c with different numbers or at different positions. The incorporation of Ac 5 c into peptides enhanced their α-helicities; however, in contrast to our expectations, it did not result in stable coiled coil formation. The structures of side chains in hydrophobic amino acids, not α-helicities appeared to be important for stable hydrophobic interactions between peptides. Although we were unable to develop coiled coil peptides with high binding affinities, the present results will be useful for designing novel coiled coil peptides. [ABSTRACT FROM AUTHOR]

Two new synthetic ionophores in which the hydrophobic portion is represented by a short helical Aib-peptide (Aib = α-amino-isobutyric acid) and the hydrophilic one is a poly-amino ( 1a ) or a polyether ( 1b ) chain have been prepared. The two conjugates show a high ionophoric activity in phospholipid membranes being able to efficiently dissipate a pH gradient and, in the case of 1b , to transport Na + across the membrane. Bioactivity evaluation of the two conjugates shows that 1a has a moderate antimicrobial activity against a broad spectrum of microorganisms and it is able to permeabilize the inner and the outer membrane of Escherichia coli cells. [ABSTRACT FROM AUTHOR]

Three types of stabilized helical peptides containing disulfide bonds, C–C cross-linked side chains, or α,α-disubstituted amino acids (2-aminoisobutyric acid (Aib)) were designed and synthesized as inhibitors of estrogen receptor (ER)-coactivator interactions. Furthermore, heptaarginine (R7)-conjugated versions of the peptides were prepared, and their effects on ER-mediated transcription were evaluated at the cellular level (in ER-positive T47D cells). Among them, the R7-conjugated peptides 11 and 12 downregulated the mRNA expression of pS2 (an ER-mediated gene whose expression is upregulated by 17β-estradiol) by 95% (at a dose of 10 μM) and 87% (at a dose of 3 μM), respectively. [ABSTRACT FROM AUTHOR]

While most proteins unfold under high-pressure conditions, some high-pressure experiments suggest that an AK16 peptide forms more helical structures. In order to understand this abnormality, molecular dynamics simulations with the simulated tempering method for the isobaric–isothermal ensemble were performed in a wide pressure range from 0.1 MPa to 1.4 GPa. It was found that the fraction of the folded state decreases once and increases after that with increasing pressure. The partial molar volume change from the folded state to unfolded state increases monotonically from a negative value to a positive value with pressure. The behaviour under high-pressure conditions is consistent with the experimental results. The radius of gyration of highly helical structures decreases with increasing pressure. Moreover, interatomic distances of AK16 become shorter at high pressure than at low pressure. These behaviours indicate that the helical structures are squeezed by high pressure. [ABSTRACT FROM AUTHOR]