Mixed Stereochemistry Macrocycle Acts as a Helix-Stabilizing Peptide N-Cap

Interactions between proteins and α-helical peptides have been the focus of drug discovery campaigns. However, the large interfaces formed between multiple turns of an α-helix and a binding protein represent a significant challenge to inhibitor discovery. Modified peptides featuring helix-stabilizing macrocycles have shown promise as inhibitors of these interactions. Here, we tested the ability of N-terminal to side-chain thioether-cyclized peptides to inhibit the α-helix binding protein Mcl-1, by screening a trillion-scale library. The enriched peptides were lariats featuring a small, four-amino-acid N-terminal macrocycle followed by a short linear sequence that resembled the natural α-helical Mcl-1 ligands. These "Heliats" (helical lariats) bound Mcl-1 with tens of nM affinity, and inhibited the interaction between Mcl-1 and a natural peptide ligand. Macrocyclization was found to stabilize α-helical structures and significantly contribute to affinity and potency. Yet, the 2nd and 3rd positions within the macrocycle were permissible to sequence variation, so that a minimal macrocyclic motif, of an N-acetylated d-phenylalanine at the 1st position thioether connected to a cysteine at the 4th, could be grafted into a range of peptides and stabilize helical conformations. We found that d-stereochemistry is more helix-stabilizing than l- at the 1st position in the motif, as the d-amino acid can utilize polyproline II torsional angles that allow for more optimal intrachain hydrogen bonding. This mixed stereochemistry macrocyclic N-cap is synthetically accessible, requiring only minor modifications to standard solid-phase peptide synthesis, and its compatibility with peptide screening can provide ready access to helix-focused peptide libraries for de novo inhibitor discovery.

Thermodynamics of modulation of interaction of α-helix inducer 2, 2, 2-trifluoroethanol with lysozyme in presence of cationic, anionic and non-ionic surfactants

The interactions of anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB) and nonionic triton X-100 (TX-100) surfactants with lysozyme at pH = 2.4 have been studied individually as well as in combination with 2,2,2-trifluoroetanol (TFE). Urea has also been used in combination with surfactants. By using these combinations, efforts have been made to obtain partially folded conformations of the protein in the presence of surfactants and effect of α-helix inducer 2,2,2-trifluoroethanol on these intermediate states. Thermodynamic analysis of all these interactions has been done employing a combination of UV-visible, fluorescence and circular dichroism spectroscopies. The results have been correlated with each other and characterized qualitatively as well as quantitatively. At lower concentration of surfactant, the thermodynamic parameters indicated the destabilizing effect of SDS, stabilizing effect of CTAB and unappreciable destabilizing impact of TX-100 on lysozyme. The enhancement in destabilization effect or reduction in stabilization effect of surfactants on lysozyme in the presence of TFE and urea has also been indicated.Communicated by Ramaswamy H. Sarma.

The effect of different conditioning agents on dentin roughness and collagen structure

OBJECTIVES

To assess the impact of various organic and inorganic acids on the roughness, demineralization, and collagen secondary structures of human dentin and to compare these effects with those of traditional agents, specifically phosphoric acid (PA) and ethylenediaminetetraacetic acid (EDTA).

METHODS

Coronal dentin discs (n = 10) were examined by optical profilometry (roughness) and ATR-FTIR before and after conditioning with 32 % PA, 3 % nitric acid (NA), 20 % citric acid (CA), 20 % phytic acid (IP6) or 17 % EDTA. Spectra data were processed to quantify dentin demineralization (DM%) and percentage area of amide I curve-fitted components of β-turns, 310-helix, α-helix, random coils, β-sheets, and collagen maturation index. Statistical analysis was performed by one-way ANOVA or Kruskal-Wallis for DM% and roughness parameters, and paired t-test/Wilcoxon test for amide I components at significance level set at α = 0.05.

RESULTS

All treatments resulted in increased roughness parameters, with the most significant changes occurring primarily with PA, while EDTA exhibited the least changes. DM% was NA>PA>IP6>CA>EDTA in a descending order. Regarding amide I components, NA demonstrated a significant reduction in β-turns, 310-helices, and α-helices and it increased β-sheets and random coils. PA resulted in reduction in β-turns and α-helices while it increased β-sheets. CA and EDTA did not cause significant changes. The collagen maturation index significantly increased only after IP6 treatment.

CONCLUSIONS

The effect on dentin roughness parameters, demineralization, and collagen secondary structures varied based on the type of dentin surface treatment.

CLINICAL SIGNIFICANCE

Understanding the impact of acids on the intrinsic properties of dentin is clinically essential for gaining insights into how these effects influence adhesion to dentin, the long-term stability of resin-based restorations, and the success of remineralization therapies.

Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains

Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated the expression pattern, structure within the ribosome and effect on protein synthesis of the ribosomal protein paralog 39L (RPL39L). With a novel mass spectrometric approach we revealed the expression of RPL39L protein beyond mouse germ cells, in human pluripotent cells, cancer cell lines and tissue samples. We generated RPL39L knock-out mouse embryonic stem cell (mESC) lines and demonstrated that RPL39L impacts the dynamics of translation, to support the pluripotency and differentiation, spontaneous and along the germ cell lineage. Most differences in protein abundance between WT and RPL39L KO lines were explained by widespread autophagy. By CryoEM analysis of purified RPL39 and RPL39L-containing ribosomes we found that, unlike RPL39, RPL39L has two distinct conformations in the exposed segment of the nascent peptide exit tunnel, creating a distinct hydrophobic patch that has been predicted to support the efficient co-translational folding of alpha helices. Our study shows that ribosomal protein paralogs provide switchable modular components that can tune translation to the protein production needs of individual cell types.

Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding

Protein conformations in cells are not solely determined by amino acid sequences; they also depend on cellular environments. For instance, the ribosome tunnel induces its specific α-helix formation during cotranslational folding. Owing to the link between these temporally α-helix and biological functions, the mechanism of α-helix formation inside the ribosome tunnel has been previously explored. Consequently, the conformational restrictions of the tunnel were considered one of the driving forces of α-helix formation. Conversely, the ribosomal tunnel environment, including its chemical properties, appears to influence the α-helix formation. However, a comprehensive analysis of the ribosome tunnel environment's impact on the α-helix formation has not been conducted yet due to challenges in experimentally controlling it. Therefore, as a new computational approach, we proposed a ribosome environment-mimicking model (REMM) based on the radius and components of the experimentally determined ribosome tunnel structures. Using REMM, we assessed the impact of the ribosome tunnel environment on α-helix formation. Herein, we employed carbon nanotubes (CNT) as a reference model alongside REMM because CNT reproduce conformational restrictions rather than the ribosome tunnel environment. Quantitatively, the ability to reproduce the α-helix of nascent peptides in the experimental structure was compared between the CNT and REMM using enhanced all-atom molecular dynamics simulations. Consequently, the REMM more accurately reproduced the α-helix of the nascent peptides than the CNT, highlighting the significance of the ribosome tunnel environment in α-helix formation. Additionally, we analyzed the properties of the peptide inside each model to reveal the mechanism of ribosome tunnel-specific α-helix formation. Consequently, we revealed that the chemical diversities of the tunnel are essential for the formation of backbone-to-backbone hydrogen bonds in the peptides. In conclusion, the ribosome tunnel environment, with the diverse chemical properties, drives its specific α-helix formation. By proposing REMM, we newly provide the technical basis for investigating the protein conformations in various cellular environments.

Exo-chirality of the α-helix

The structure of helical polymers is dictated by the molecular chirality of their monomer units. Particularly, macromolecular helices with monomer sequence control have the potential to generate chiral topologies. In α-helical folded peptides, the sequential repetition of amino acids generates a chiral layer defined by the amino acid side chains projected outside the amide backbone. Despite being closely related to peptides' structural and functional properties, to the best of our knowledge, a general exo-helical symmetry model has not been yet described for the α-helix. Here, we perform the theoretical, computational, and spectroscopic elucidation of the α-helix principal exo-helical topologies. Non-canonical labeled amino acids are employed to spectroscopically characterize the different exo-helical topologies in solution, which precisely match the theorical prediction. Backbone-to-chromophore distance also shows the expected impact in the exo-helices' geometry and spectroscopic fingerprint. Theoretical prediction and spectroscopic validation of this exo-helical topological model provides robust experimental evidence of the chiral potential on the surface of helical peptides and outlines an entirely new structural scenario for the α-helix.

Structural insights into the Langya virus attachment glycoprotein

Langya virus (LayV) was recently detected in patients with acute pneumonic diseases in China. Genome alignment indicated that LayV is a type of zoonotic henipavirus (HNV) that might also infect domestic animals. Previous studies revealed that HNVs mainly use ephrin-B1, ephrin-B2, or ephrin-B3 as cell receptors and the attachment glycoprotein (G) is the host cell receptor-binding protein. However, the LayV receptor remains unknown. Here, we present the 2.77 Å crystal structure of the LayV G C-terminal domain (CTD). We show that the LayV G protein CTD possesses a similar architecture as the Mojiang virus (MojV) G protein but is markedly different from the Nipah virus (NiV), Hendra virus (HeV), and Cedar virus (CedV) G proteins. Surface plasmon resonance (SPR) experiments indicate that LayV G does not bind ephrin-B proteins. Steric hindrance may prevent interactions between LayV G and ephrin-B. Our data might facilitate drug development targeting LayV.

The Pathway of a Transmembrane Helix Insertion into the Membrane Assisted by Sec61α Channel

The significant inconsistency between the experimental and simulation results of the free energy for the translocon-assisted insertion of the transmembrane helix (TMH) has not been reasonably explained. Understanding the mechanism of TMH insertion through the translocon is the key to solving this problem. In this study, we performed a series of coarse-grained molecular dynamics simulations and calculated the potential mean forces (PMFs) for three insertion processes of a hydrophobic TMH. The simulations reveal the pathway of the TMH insertion assisted by a translocon. The results indicate that the TMH contacts the top of the lateral gate first and then inserts down the lateral gate, which agrees with the sliding model. The TMH begins to transfer laterally to the bilayer when it is blocked by the plug and reaches the exit of the lateral gate, where there is a free energy minimum point. We also found that the connecting section between TM2 and TM3 of Sec61α prevented TMH from leaving the lateral gate and directly transitioning to the surface-bound state. These findings provide insight into the mechanism of the insertion of TMH through the translocon.

Rationally seeded computational protein design of ɑ-helical barrels

Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of α-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix-turn-helix-turn-helix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression in Escherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy.

Insight into the autoproteolysis mechanism of the RsgI9 anti-σ factor from Clostridium thermocellum

Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass-sensing RsgI-type anti-σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti-σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn-Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti-σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Structural basis for the recognition of α-1,6-branched α-glucan by GH13_47 α-amylase from Rhodothermus marinus

Glycoside hydrolase (GH) family 13 is among the main families of enzymes acting on starch; recently, subfamily 47 of GH13 (GH13_47) has been established. The crystal structure and function of a GH13_47 enzyme from Bacteroides ovatus has only been reported to date. This enzyme has α-amylase activity, while the GH13_47 enzymes comprise approximately 800-900 amino acid residues which are almost double those of typical α-amylases. It is important to know how different the GH13_47 enzymes are from other α-amylases. Rhodothermus marinus JCM9785, a thermophilic bacterium, possesses a gene for the GH13_47 enzyme, which is designated here as RmGH13_47A. Its structure has been predicted to be composed of seven domains: N1, N2, N3, A, B, C, and D. We constructed a plasmid encoding Gly266-Glu886, which contains the N3, A, B, and C domains and expressed the protein in Escherichia coli. The enzyme hydrolyzed starch and pullulan by a neopullulanase-type action. Additionally, the enzyme acted on maltotetraose, and saccharides with α-1,6-glucosidic linkages were observed in the products. Following the replacement of the catalytic residue Asp563 with Ala, the crystal structure of the variant D563A in complex with the enzymatic products from maltotetraose was determined; as a result, electron density for an α-1,6-branched pentasaccharide was observed in the catalytic pocket, and Ile762 and Asp763 interacted with the branched chain of the pentasaccharide. These findings suggest that RmGH13_47A is an α-amylase that prefers α-1,6-branched parts of starch to produce oligosaccharides.

Unraveling the binding mechanism between soybean protein isolate and selected bioactive compounds

The present study was aimed to investigate the interactions between soybean protein isolate (SPI) with resveratrol (RESV) and lutein (LUT). The binding forces, molecular interactions and functional properties were explored by multi-spectroscopic analysis, molecular docking and functional property indexes between SPI and RESV/LUT. The RESV/LUT quenched SPI chromophore residues with static mechanism and the endothermic reaction. The SPI- RESV/LUT complexes were formed through hydrogen bond, electrostatic and hydrophobic interactions. Molecular docking confirmed van-der-Waals force as one of the important forces. The interaction of RESV/LUT led to SPI's secondary structure alterations with a decrease in α-helix and random coil and an increase in β-sheet and β-turns. RESV/LUT developed foaming and emulsifying properties of SPI and showed a significant decrease of the surface hydrophobicity with RESV/LUT concentrations increase attributed to SPI's partial unfolding. Our study exposed molecular mechanisms and confirmations to understand the interactions in protein- RESV/LUT complexes for protein industrial base promotion.

Modification of soy protein isolate and pea protein isolate by high voltage dielectric barrier discharge (DBD) atmospheric cold plasma: Comparative study on structural, rheological and techno-functional characteristics

The modification in structural, rheological, and techno-functional characteristics of soy and pea protein isolates (SPI and PPI) due to dielectric barrier discharge cold plasma (DBD-CP) were assessed. The increased carbonyl groups in both samples with cold plasma (CP) treatment led to a reduction in free sulfhydryl groups. Moreover, protein solubility of treated proteins exhibited significant improvements, reaching up to 59.07 % and 41.4 % for SPI and PPI, respectively, at 30 kV for 8 min. Rheological analyses indicated that storage modulus (G') was greater than loss modulus (G″) for CP-treated protein gels. Furthermore, in vitro protein digestibility of SPI exhibited a remarkable improvement (4.78 %) at 30 kV for 6 min compared to PPI (3.23 %). Spectroscopic analyses, including circular dichroism and Fourier Transform-Raman, indicated partial breakdown and loss of α-helix structure in both samples, leading to the aggregation of proteins. Thus, DBD-CP induces reactive oxygen species-mediated oxidation, modifying the secondary and tertiary structures of samples.

High amphipathicity of α-helical peptides enhances unmethylated CpG DNA-induced activation of mouse macrophage-like RAW264.7 cells

The α-helical antimicrobial peptide Kn2-7 enhances the activation of mouse macrophage-like RAW264.7 induced by DNA containing unmethylated cytosine-guanine motifs (CpG DNA). This enhancement is related to increased cellular uptake of DNA by Kn2-7, but the relevant properties of Kn2-7 are unknown. Physicochemical property analysis revealed that Kn2-7 has high amphipathicity. In contrast, the α-helical antimicrobial peptide L5, which increases the cellular uptake of CpG DNA but does not enhance CpG DNA-induced activation, has low amphipathicity. Kn2-7 derivatives with decreased amphipathicity but the same amino acid composition as Kn2-7 did not enhance CpG DNA-induced activation. On the other hand, L5 derivatives with high amphipathicity but the same amino acid composition as L5 enhanced CpG DNA-induced activation. Cellular uptake of DNA was not increased by the L5 derivatives, indicating that high amphipathicity does not affect DNA uptake. Furthermore, α-helical peptides with reversed sequences relative to the Kn2-7 and L5 derivatives with high amphipathicity were synthesized. The reversed-sequence peptides, which had the same amphipathicity but different amino acid sequences from their counterparts, enhanced CpG DNA-induced activation. Taken together, these observations indicate that the high amphipathicity of α-helical peptides enhances the CpG DNA-induced activation of RAW264.7.

Antimicrobial Activity of Positively Charged Oligopeptides with Theoretical High α-Helix Content against Cutibacterium acnes

Cutibacterium acnes is abundant and commonly exists as a superficial bacteria on human skin. Recently, the resistance of C. acnes to antimicrobial agents has become a serious concern, necessitating the development of alternative pharmaceutical products with antimicrobial activity against C. acnes. To address this need, we evaluated the antimicrobial activity of CKR-13-a mutant oligopeptide of FK-13 with increased net charge and theoretical α-helical content-against C. acnes in modified Gifu Anaerobic Medium broth by determining the minimum inhibitory concentration (MIC). CKR-13 exerted greater antimicrobial activity against C. acnes than FK-13 in the broth at pH 7.0. The antimicrobial activity of CKR-13 with RXM against C. albicans was pH-dependent. The ionization of CKR-13 and pH-dependent growth delay of C. albicans was suggested to be associated with the increase in CKR-13 antimicrobial activity.

Functionally Active Synthetic α-Helical Pores

ConspectusTransmembrane pores are currently at the forefront of nanobiotechnology, nanopore chemistry, and synthetic chemical biology research. Over the past few decades, significant studies in protein engineering have paved the way for redesigning membrane protein pores tailored for specific applications in nanobiotechnology. Most previous efforts predominantly centered on natural β-barrel pores designed with atomic precision for nucleic acid sequencing and sensing of biomacromolecules, including protein fragments. The requirement for a more efficient single-molecule detection system has driven the development of synthetic nanopores. For example, engineering channels to conduct ions and biomolecules selectively could lead to sophisticated nanopore sensors. Also, there has been an increased interest in synthetic pores, which can be fabricated to provide more control in designing architecture and diameter for single-molecule sensing of complex biomacromolecules. There have been impressive advancements in developing synthetic DNA-based pores, although their application in nanopore technology is limited. This has prompted a significant shift toward building synthetic transmembrane α-helical pores, a relatively underexplored field offering novel opportunities. Recently, computational tools have been employed to design and construct α-helical barrels of defined structure and functionality.We focus on building synthetic α-helical pores using naturally occurring transmembrane motifs of membrane protein pores. Our laboratory has developed synthetic α-helical transmembrane pores based on the natural porin PorACj (Porin A derived from Corynebacterium jeikeium) that function as nanopore sensors for single-molecule sensing of cationic cyclodextrins and polypeptides. Our breakthrough lies in being the first to create a functional and large stable synthetic transmembrane pore composed of short synthetic α-helical peptides. The key highlight of our work is that these pores can be synthesized using easy chemical synthesis, which permits its easy modification to include a variety of functional groups to build charge-selective sophisticated pores. Additionally, we have demonstrated that stable functional pores can be constructed from D-amino acid peptides. The analysis of pores composed of D- and L-amino acids in the presence of protease showed that only the D pores are highly functional and stable. The structural models of these pores revealed distinct surface charge conformation and geometry. These new classes of synthetic α-helical pores are highly original systems of general interest due to their unique architecture, functionality, and potential applications in nanopore technology and chemical biology. We emphasize that these simplified transmembrane pores have the potential to be components of functional nanodevices and therapeutic tools. We also suggest that such designed peptides might be valuable as antimicrobial agents and can be targeted to cancer cells. This article will focus on the evolutions in assembling α-helical transmembrane pores and highlight their advantages, including structural and functional versatility.

Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity

Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic "isoprenol pathways," which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non-natural alkyl-monophosphates (alkyl-Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids with potentially useful activities. However, only a handful of IPK crystal structures have been solved to date, and even fewer of these contain non-natural substrates bound in the active site. The current study sought to elucidate additional ternary complexes bound to non-natural substrates using the IPK homolog from Thermococcus paralvinellae (TcpIPK). Four such structures were solved, each bound to a different non-natural alkyl-P and the phosphoryl donor substrate/product adenosine triphosphate (ATP)/adenosine diphosphate (ADP). As expected, the quaternary, tertiary, and secondary structures of TcpIPK closely resembled those of IPKs published previously, and kinetic analysis of a novel alkyl-P substrate highlighted the potentially dramatic effects of altering the core scaffold of the natural substrate. Even more interesting, though, was the discovery of a trend correlating the position of two α helices in the active site with the magnitude of an IPK homolog's reaction rate for the natural reaction. Overall, the current structures of TcpIPK highlight the importance of continued structural analysis of the IPKs to better understand and optimize their activity with both natural and non-natural substrates.

Transmembrane helix interactions regulate oligomerization of the receptor tyrosine kinase EphA2

The transmembrane helices of receptor tyrosine kinases (RTKs) have been proposed to switch between two different dimeric conformations, one associated with the inactive RTK and the other with the active RTK. Furthermore, recent work has demonstrated that some full-length RTKs are associated into oligomers that are larger than dimers, raising questions about the roles of the TM helices in the assembly and function of these oligomers. Here we probe the roles of the TM helices in the assembly of EphA2 RTK oligomers in the plasma membrane. We employ mutagenesis to evaluate the relevance of a published NMR dimeric structure of the isolated EphA2 TM helix in the context of the full-length EphA2 in the plasma membrane. We use two fluorescence methods, Förster Resonance Energy Transfer and Fluorescence Intensity Fluctuations spectrometry, which yield complementary information about the EphA2 oligomerization process. These studies reveal that the TM helix mutations affect the stability, structure, and size of EphA2 oligomers. However, the effects are multifaceted and point to a more complex role of the TM helix than the one expected from the "TM dimer switch" model.

Effect of L-cysteine on the physicochemical properties of heat-induced sheep plasma protein gels

The effects of different l-Cysteine additions (0-2 %) on the gel properties, microstructure and physicochemical stability of sheep plasma protein gels were studied. The introduction of l-Cys significantly improved the water retention capacity and whiteness of the plasma protein gel (p < 0.05). The addition of 0.2 %-0.4 % l-Cys increased gel strength, but l-Cys had no significant effect on gel elasticity (p < 0.05). Scanning electron microscopy confirmed that the addition of l-Cys also promoted the formation of a porous three-dimensional network structure in the gel. Raman spectroscopy and SDS-PAGE revealed that the addition of l-Cys generally reduced α-helix structures in protein gels and promoted the formation of β-folds. Addition of 0.2 % l-Cys treatment leading to the greatest increase in disulfide bonds, and its surface hydrophobicity and endogenous fluorescence intensity were the largest. At this time, the comprehensive performance of sheep plasma protein gel is the best performance.

Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I

Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.

Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy

The Davydov model was conjectured to describe how an amide I excitation created during ATP hydrolysis in myosin might be significant in providing energy to drive myosin's chemomechanical cycle. The free energy surfaces of the myosin relay helix peptide dissolved in 2,2,2-trifluoroethanol (TFE), determined by metadynamics simulations, demonstrate local minima differing in free energy by only ~2 kT, corresponding to broken and stabilized hydrogen bonds, respectively. Experimental pump-probe and 2D infrared spectroscopy were performed on the peptide dissolved in TFE. The relative heights of two peaks seen in the pump-probe data and the corresponding relative volumes of diagonal peaks seen in the 2D-IR spectra at time delays between 0.5 ps and 1 ps differ noticeably from what is seen at earlier or later time delays or in the linear spectrum, indicating that a vibrational excitation may influence the conformational state of this helix. Thus, it is possible that the presence of an amide I excitation may be a direct factor in the conformational state taken on by the myosin relay helix following ATP hydrolysis in myosin.

Design and Function of α-Helix-Rich, Heme-Binding Peptide Materials

Peptide materials often employ short peptides that self-assemble into unique nanoscale architectures and have been employed across many fields relevant to medicine and energy. A majority of peptide materials are high in β-sheet, secondary structure content, including heme-binding peptide materials. To broaden the structural diversity of heme-binding peptide materials, a small series of peptides were synthesized to explore the design criteria required for (1) folding into an α-helix structure, (2) assembling into a nanoscale material, (3) binding heme, and (4) demonstrating functions similar to that of heme proteins. One peptide was identified to meet all four criteria, including the heme protein function of CO binding and its microsecond-to-millisecond recombination rates, as measured by transient absorption spectroscopy. Implications of new design criteria and peptide material function through heme incorporation are discussed.

Molecular mechanism of substrate recognition and cleavage by human γ-secretase

Successive cleavages of amyloid precursor protein C-terminal fragment with 99 residues (APP-C99) by γ-secretase result in amyloid-β (Aβ) peptides of varying lengths. Most cleavages have a step size of three residues. To elucidate the underlying mechanism, we determined the atomic structures of human γ-secretase bound individually to APP-C99, Aβ49, Aβ46, and Aβ43. In all cases, the substrate displays the same structural features: a transmembrane α-helix, a three-residue linker, and a β-strand that forms a hybrid β-sheet with presenilin 1 (PS1). Proteolytic cleavage occurs just ahead of the substrate β-strand. Each cleavage is followed by unwinding and translocation of the substrate α-helix by one turn and the formation of a new β-strand. This mechanism is consistent with existing biochemical data and may explain the cleavages of other substrates by γ-secretase.

Inducing α-Helicity in Peptides by Silver Coordination to Cysteine

Short peptide sequences consisting of two cysteine residues separated by three other amino acids display complete change from random coil to α-helical secondary structure in response to addition of Ag+ ions. The folded CXXXC/Ag+ complex involves formation of multinuclear Ag+ species and is stable in a wide pH range from below 3 to above 8. The complex is stable through reversed-phase HPLC separation as well as towards a physiological level of chloride ions, based on far-UV circular dichroism spectroscopy. In electrospray MS under acidic conditions a peptide dimer with four Ag+ ions bound was observed, and modelling based on potentiometric experiments supported this to be the dominating complex at neutral pH together with a peptide dimer with 3 Ag+ and one proton at lower pH. The complex was demonstrated to work as a N-terminal nucleation site for inducing α-helicity into longer peptides. This type of silver-mediated peptide assembly and folding may be of more general use for stabilizing not only peptide folding but also for controlling oligomerization even under acidic conditions.