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1.
ACS Nano ; 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-39008647

ABSTRACT

Magnetic field-directed colloidal interactions offer facile tools for assembly of structures that range from linear chains to multidimensional hierarchical architectures. While the field-driven assembly of colloidal particles has commonly been investigated in unbounded media, a knowledge gap remains concerning such assembly in confined microenvironments. Here, we investigate how confinement of ferromagnetic nanoparticles in microspheres directs their magnetic assembly into hierarchical architectures. Microdroplets from polydimethylsiloxane (PDMS) liquid precursor containing dispersed iron oxide magnetic nanoparticles (MNPs) were placed in a static magnetic field leading to the formation of organized assemblies inside the host droplets. By changing the MNP concentrations, we revealed a sequence of microstructures inside the droplets, ranging from linear chains at a low MNP loading, transitioning to a combination of chains and networked bundles, to solely 3D bundles at high MNP loading. These experimental results were analyzed with the aid of COMSOL simulations where we calculated the potential energy to identify the preferred assembly conformations. The chains at high MNP loading minimized their energy by aggregating laterally to form bundles with their MNP dipoles being out-of-registry. We cured these PDMS droplets to immobilize the assemblies by forming soft microbeads. These microbeads constitute an "interaction toolbox" with different magnetic macroscale responses, which are governed by the structuring of the MNPs and their magnetic polarizability. We show that thanks to their ability to rotate by field-induced torque under a rotating field, these microbeads can be employed in applications such as optical modulators and microrollers.

2.
PLoS Comput Biol ; 19(12): e1011685, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38048311

ABSTRACT

Co-assembling peptides can be crafted into supramolecular biomaterials for use in biotechnological applications, such as cell culture scaffolds, drug delivery, biosensors, and tissue engineering. Peptide co-assembly refers to the spontaneous organization of two different peptides into a supramolecular architecture. Here we use molecular dynamics simulations to quantify the effect of anionic amino acid type on co-assembly dynamics and nanofiber structure in binary CATCH(+/-) peptide systems. CATCH peptide sequences follow a general pattern: CQCFCFCFCQC, where all C's are either a positively charged or a negatively charged amino acid. Specifically, we investigate the effect of substituting aspartic acid residues for the glutamic acid residues in the established CATCH(6E-) molecule, while keeping CATCH(6K+) unchanged. Our results show that structures consisting of CATCH(6K+) and CATCH(6D-) form flatter ß-sheets, have stronger interactions between charged residues on opposing ß-sheet faces, and have slower co-assembly kinetics than structures consisting of CATCH(6K+) and CATCH(6E-). Knowledge of the effect of sidechain type on assembly dynamics and fibrillar structure can help guide the development of advanced biomaterials and grant insight into sequence-to-structure relationships.


Subject(s)
Nanofibers , Nanofibers/chemistry , Molecular Dynamics Simulation , Amino Acids , Peptides/chemistry , Biocompatible Materials
3.
J Chem Theory Comput ; 19(24): 9457-9467, 2023 Dec 26.
Article in English | MEDLINE | ID: mdl-37937823

ABSTRACT

Peptoids, or N-substituted glycines, are peptide-like materials that form a wide variety of secondary structures owing to their enhanced flexibility and a diverse collection of possible side chains. Compared to that of peptides, peptoids have a substantially more complex conformational landscape. This is mainly due to the ability of the peptoid amide bond to exist in both cis- and trans-conformations. This makes conventional molecular dynamics simulations and even some enhanced sampling approaches unable to sample the complete energy landscapes. In this article, we present an extension to the CGenFF-NTOID peptoid atomistic forcefield by adding parameters for four side chains to the previously available collection. We employ explicit solvent well-tempered metadynamics simulations to optimize our forcefield parameters and parallel bias metadynamics to study the cis-trans isomerism for SN1-phenylethyl (s1pe) and SN1-naphthylethyl (s1ne) peptoid monomers, the free energy minima generated from which are validated with available experimental data. In the absence of experimental data, we supported our atomistic simulations with ab initio calculations. This work represents an important step toward the computational design of peptoid-based materials.

4.
Angew Chem Int Ed Engl ; 62(51): e202314531, 2023 Dec 18.
Article in English | MEDLINE | ID: mdl-37931093

ABSTRACT

Self-assembly of proteinaceous biomolecules into functional materials with ordered structures that span length scales is common in nature yet remains a challenge with designer peptides under ambient conditions. This report demonstrates how charged side-chain chemistry affects the hierarchical co-assembly of a family of charge-complementary ß-sheet-forming peptide pairs known as CATCH(X+/Y-) at physiologic pH and ionic strength in water. In a concentration-dependent manner, the CATCH(6K+) (Ac-KQKFKFKFKQK-Am) and CATCH(6D-) (Ac-DQDFDFDFDQD-Am) pair formed either ß-sheet-rich microspheres or ß-sheet-rich gels with a micron-scale plate-like morphology, which were not observed with other CATCH(X+/Y-) pairs. This hierarchical order was disrupted by replacing D with E, which increased fibril twisting. Replacing K with R, or mutating the N- and C-terminal amino acids in CATCH(6K+) and CATCH(6D-) to Qs, increased observed co-assembly kinetics, which also disrupted hierarchical order. Due to the ambient assembly conditions, active CATCH(6K+)-green fluorescent protein fusions could be incorporated into the ß-sheet plates and microspheres formed by the CATCH(6K+/6D-) pair, demonstrating the potential to endow functionality.


Subject(s)
Peptides , Protein Conformation, beta-Strand , Peptides/chemistry , Gels
5.
J Phys Chem B ; 127(39): 8370-8381, 2023 Oct 05.
Article in English | MEDLINE | ID: mdl-37735840

ABSTRACT

Peptides that bind to inorganic materials can be used to functionalize surfaces, control crystallization, or assist in interfacial self-assembly. In the past, inorganic-binding peptides have been found predominantly through peptide library screening. While this method has successfully identified peptides that bind to a variety of materials, an alternative design approach that can intelligently search for peptides and provide physical insight for peptide affinity would be desirable. In this work, we develop a computational, physics-based approach to design inorganic-binding peptides, focusing on peptides that bind to the common plastics polyethylene, polypropylene, polystyrene, and poly(ethylene terephthalate). The PepBD algorithm, a Monte Carlo method that samples peptide sequence and conformational space, was modified to include simulated annealing, relax hydration constraints, and an ensemble of conformations to initiate design. These modifications led to the discovery of peptides with significantly better scores compared to those obtained using the original PepBD. PepBD scores were found to improve with increasing van der Waals interactions, although strengthening the intermolecular van der Waals interactions comes at the cost of introducing unfavorable electrostatic interactions. The best designs are enriched in amino acids with bulky side chains and possess hydrophobic and hydrophilic patches whose location depends on the adsorbed conformation. Future work will evaluate the top peptide designs in molecular dynamics simulations and experiment, enabling their application in microplastic pollution remediation and plastic-based biosensors.

6.
Commun Biol ; 6(1): 878, 2023 08 26.
Article in English | MEDLINE | ID: mdl-37634026

ABSTRACT

Infections by Clostridioides difficile, a bacterium that targets the large intestine (colon), impact a large number of people worldwide. Bacterial colonization is mediated by two exotoxins: toxins A and B. Short peptides that can be delivered to the gut and inhibit the biocatalytic activity of these toxins represent a promising therapeutic strategy to prevent and treat C. diff. infection. We describe an approach that combines a Peptide Binding Design (PepBD) algorithm, molecular-level simulations, a rapid screening assay to evaluate peptide:toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells. One peptide, SA1, is found to block TcdA toxicity in primary-derived human colon (large intestinal) epithelial cells. SA1 binds TcdA with a KD of 56.1 ± 29.8 nM as measured by surface plasmon resonance (SPR).


Subject(s)
Clostridioides difficile , Humans , Colon , Algorithms , Biocatalysis , Peptides/pharmacology
7.
Soft Matter ; 19(22): 4123-4136, 2023 Jun 07.
Article in English | MEDLINE | ID: mdl-37249009

ABSTRACT

Colloidal particles with anisotropic shapes and interactions display rich phase behavior and have potential as structural bases for materials with controllable properties. In this paper, we explore the self-assembling characteristics of a new class of particles that have been shown experimentally to form reconfigurable structures: microscopic cube-shaped colloids with a magnetic dipole that is transversely offset from the particle's center of mass. We have performed in silico simulations of the dynamics of large numbers of dipolar squares in two-dimensions using discontinuous molecular dynamics (DMD). We use a coarse-grain method where the dipolar microcubes are represented by a group of four hard circles bonded together to create a rigid square in two-dimensions and two opposite charges are embedded within the square to represent a magnetic dipole. Annealing, or "slow-cooling", simulations are conducted to determine the equilibrium structures. Systems of dipolar squares tend to assemble into one of two different types of conformations: either single- or double-stranded assemblies, each with unique structures and phase diagrams in the temperature-density plane. Single-stranded assemblies form highly interconnected percolated, or gel-like, networks. In contrast, double stranded assemblies tend to form globally-aligned nematic states at high densities, although this is not seen consistently in all runs. The phase behavior of systems of dipolar squares depends not only on the system's temperature and density, but also on the type of dipole embedded within the square and on the relative number of squares with an opposite "handedness" that are present within the system.

8.
Appl Biosaf ; 28(1): 22-31, 2023 Mar 01.
Article in English | MEDLINE | ID: mdl-36895584

ABSTRACT

Introduction: Emergency preparedness is not a novel topic. What has been novel is the fast pace at which organizations, including academic institutions, have had to adapt to infectious disease outbreaks since 2000. Objective: The goal of this article is to highlight the various environmental health and safety (EHS) team activities during the coronavirus disease 2019 (COVID-19) pandemic to ensure that on-site personnel was safe, the research could be conducted, and critical business operations such as academics, laboratory animal care, environmental compliance, and routine healthcare functions could continue during the pandemic. Methods: The response framework is presented by discussing first the lessons learned in preparedness and emergency response during outbreaks that occurred since 2000, namely Influenza virus, Zika virus, and Ebola virus. Then, how the response to the COVID-19 pandemic was activated, and the effects of ramping down research and business activities. Results: Next, the contributions of each EHS unit are presented, namely, environmental, industrial hygiene and occupational safety, research safety and biosafety, radiation safety, supporting healthcare activities, disinfection, and communications and training. Discussion: Lastly, a few lessons learned are shared with the reader for moving toward normalcy.

9.
bioRxiv ; 2023 Jan 12.
Article in English | MEDLINE | ID: mdl-36711911

ABSTRACT

Clostridioides difficile ( C. diff .) is a bacterium that causes severe diarrhea and inflammation of the colon. The pathogenicity of C. diff . infection is derived from two major toxins, toxins A (TcdA) and B (TcdB). Peptide inhibitors that can be delivered to the gut to inactivate these toxins are an attractive therapeutic strategy. In this work, we present a new approach that combines a pep tide b inding d esign algorithm (PepBD), molecular-level simulations, rapid screening of candidate peptides for toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block the glucosyltransferase activity of TcdA by targeting its glucosyltransferase domain (GTD). Using PepBD and explicit-solvent molecular dynamics simulations, we identified seven candidate peptides, SA1-SA7. These peptides were selected for specific TcdA GTD binding through a custom solid-phase peptide screening system, which eliminated the weaker inhibitors SA5-SA7. The efficacies of SA1-SA4 were then tested using a trans-epithelial electrical resistance (TEER) assay on monolayers of the human gut epithelial culture model. One peptide, SA1, was found to block TcdA toxicity in primary-derived human jejunum (small intestinal) and colon (large intestinal) epithelial cells. SA1 bound TcdA with a K D of 56.1 ± 29.8 nM as measured by surface plasmon resonance (SPR). Significance Statement: Infections by Clostridioides difficile , a bacterium that targets the large intestine (colon), impact a significant number of people worldwide. Bacterial colonization is mediated by two exotoxins: toxins A and B. Short peptides that can inhibit the biocatalytic activity of these toxins represent a promising strategy to prevent and treat C. diff . infection. We describe an approach that combines a Peptide B inding D esign (PepBD) algorithm, molecular-level simulations, a rapid screening assay to evaluate peptide:toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in small intestinal and colon epithelial cells. Importantly, our designed peptide, SA1, bound toxin A with nanomolar affinity and blocked toxicity in colon cells.

10.
J Phys Chem B ; 126(41): 8129-8139, 2022 10 20.
Article in English | MEDLINE | ID: mdl-36219223

ABSTRACT

The COVID-19 pandemic has caused significant social and economic disruption across the globe. Cellular entry of SARS-CoV-2 into the human body is mediated via binding of the Receptor Binding Domain (RBD) on the viral Spike protein (SARS-CoV-2 RBD) to Angiotensin-Converting Enzyme 2 (ACE2) expressed on host cells. Molecules that can disrupt ACE2:RBD interactions are attractive therapeutic candidates to prevent virus entry into human cells. A computational strategy that combines our Peptide Binding Design (PepBD) algorithm with atomistic molecular dynamics simulations was used to design new inhibitory peptide candidates via sequence iteration starting with a 23-mer peptide, referred to as SBP1. SBP1 is derived from a region of the ACE2 Peptidase Domain α1 helix that binds to the SARS-CoV-2 RBD of the initial Wuhan-Hu-1 strain. Three peptides demonstrated a solution-phase RBD-binding dissociation constant in the micromolar range during tryptophan fluorescence quenching experiments, one peptide did not bind, and one was insoluble at micromolar concentrations. However, in competitive ELISA assays, none of these peptides could outcompete ACE2 binding to SARS-CoV-2-RBD up to concentrations of 50 µM, similar to the parent SBP1 peptide which also failed to outcompete ACE2:RBD binding. Molecular dynamics simulations suggest that P4 would have a good binding affinity for the RBD domain of Beta-B.1.351, Gamma-P.1, Kappa-B.1.617.1, Delta-B.1.617.2, and Omicron-B.1.1.529 variants, but not the Alpha variant. Consistent with this, P4 bound Kappa-B.1.617.1 and Delta-B.1.617.2 RBD with micromolar affinity in tryptophan fluorescence quenching experiments. Collectively, these data show that while relatively short unstructured peptides can bind to SARS-CoV-2 RBD with moderate affinity, they are incapable of outcompeting the strong interactions between RBD and ACE2.


Subject(s)
Angiotensin-Converting Enzyme 2 , COVID-19 , Humans , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Pandemics , Tryptophan/metabolism , Protein Binding , Peptides/metabolism
11.
J Chromatogr A ; 1669: 462941, 2022 Apr 26.
Article in English | MEDLINE | ID: mdl-35303576

ABSTRACT

Antibody fragments and their engineered variants show true potential as next-generation therapeutics as they combine excellent targeting with superior biodistribution and blood clearance. Unlike full antibodies, however, antibody fragments do not yet have a standard platform purification process for large-scale production. Short peptide ligands are viable alternatives to protein ligands in affinity chromatography. In this work, an integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments. The first cohort of designed sequences was tested experimentally using human polyclonal Fab, and the top performing sequence was selected as a prototype for a subsequent round of ligand refinement in silico. The resulting peptides were conjugated to chromatographic resins and evaluated via equilibrium and dynamic binding studies using human Fab-κ and Fab-λ. The equilibrium studies returned values of binding capacities up to 32 mg of Fab per mL of resin with mild affinity (KD ∼ 10-5 M) that are conducive to high product capture and recovery. Dynamic studies returned values of product yield up to ∼90%. Preliminary purification studies provided purities of 83-93% and yields of 11-89%. These results lay the groundwork for future development of these ligands towards biomanufacturing translation.


Subject(s)
Immunoglobulin Fab Fragments , Immunoglobulin G , Humans , Immunoglobulin Fab Fragments/chemistry , Ligands , Peptides , Tissue Distribution
12.
ACS Chem Biol ; 17(1): 118-128, 2022 01 21.
Article in English | MEDLINE | ID: mdl-34965093

ABSTRACT

Clostridium difficile infection is mediated by two major exotoxins: toxins A (TcdA) and B (TcdB). Inhibiting the biocatalytic activities of these toxins with targeted peptide-based drugs can reduce the risk of C. difficile infection. In this work, we used a computational strategy that integrates a peptide binding design (PepBD) algorithm and explicit-solvent atomistic molecular dynamics simulation to determine promising toxin A-targeting peptides that can recognize and bind to the catalytic site of the TcdA glucosyltransferase domain (GTD). Our simulation results revealed that two out of three in silico discovered peptides, viz. the neutralizing peptides A (NPA) and B (NPB), exhibit lower binding free energies when bound to the TcdA GTD than the phage-display discovered peptide, viz. the reference peptide (RP). These peptides may serve as potential inhibitors against C. difficile infection. The efficacy of the peptides RP, NPA, and NPB to neutralize the cytopathic effects of TcdA was tested in vitro in human jejunum cells. Both phage-display peptide RP and in silico peptide NPA were found to exhibit strong toxin-neutralizing properties, thereby preventing the TcdA toxicity. However, the in silico peptide NPB demonstrates a relatively low efficacy against TcdA.


Subject(s)
Bacterial Toxins/antagonists & inhibitors , Computer Simulation , Enterotoxins/antagonists & inhibitors , Peptides/pharmacology , Bacterial Toxins/chemistry , Drug Design , Enterotoxins/chemistry , Models, Molecular , Peptides/chemistry , Protein Binding , Protein Conformation , Protein Domains , Reproducibility of Results
13.
PNAS Nexus ; 1(5): pgac263, 2022 Nov.
Article in English | MEDLINE | ID: mdl-36712347

ABSTRACT

Screening amino acid sequence space via experiments to discover peptides that self-assemble into amyloid fibrils is challenging. We have developed a computational peptide assembly design (PepAD) algorithm that enables the discovery of amyloid-forming peptides. Discontinuous molecular dynamics (DMD) simulation with the PRIME20 force field combined with the FoldAmyloid tool is used to examine the fibrilization kinetics of PepAD-generated peptides. PepAD screening of ∼10,000 7-mer peptides resulted in twelve top-scoring peptides with two distinct hydration properties. Our studies revealed that eight of the twelve in silico discovered peptides spontaneously form amyloid fibrils in the DMD simulations and that all eight have at least five residues that the FoldAmyloid tool classifies as being aggregation-prone. Based on these observations, we re-examined the PepAD-generated peptides in the sequence pool returned by PepAD and extracted five sequence patterns as well as associated sequence signatures for the 7-mer amyloid-forming peptides. Experimental results from Fourier transform infrared spectroscopy (FTIR), thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) indicate that all the peptides predicted to assemble in silico assemble into antiparallel ß-sheet nanofibers in a concentration-dependent manner. This is the first attempt to use a computational approach to search for amyloid-forming peptides based on customized settings. Our efforts facilitate the identification of ß-sheet-based self-assembling peptides, and contribute insights towards answering a fundamental scientific question: "What does it take, sequence-wise, for a peptide to self-assemble?".

14.
J Phys Chem B ; 125(50): 13599-13609, 2021 12 23.
Article in English | MEDLINE | ID: mdl-34905370

ABSTRACT

Peptide coassembly, wherein at least two different peptides interact to form multicomponent nanostructures, is an attractive approach for generating functional biomaterials. Current efforts seek to design pairs of peptides, A and B, that form nanostructures (e.g., ß-sheets with ABABA-type ß-strand patterning) while resisting self-assembly (e.g., AAAAA-type or BBBBB-type ß-sheets). To confer coassembly behavior, most existing designs have been based on highly charged variants of known self-assembling peptides; like-charge repulsion limits self-assembly while opposite-charge attraction promotes coassembly. Recent analyses using solid-state NMR and coarse-grained simulations reveal that preconceived notions of structure and molecular organization are not always correct. This perspective highlights recent advances and key challenges to understanding and controlling peptide coassembly.


Subject(s)
Biocompatible Materials , Nanostructures , Magnetic Resonance Spectroscopy , Peptides , Protein Conformation, beta-Strand
15.
Animals (Basel) ; 11(11)2021 Nov 12.
Article in English | MEDLINE | ID: mdl-34827960

ABSTRACT

The international governing body for equestrian sports, the Fédération Equestre Internationale (FEI), states that the welfare of the horse must be paramount and never subordinated to competitive or commercial influences. However, there is growing unease about welfare issues from both within and outside the sport. The aim of this study was to understand stakeholder perceptions of current welfare issues within equestrian sport, determine whether there is scope for change, and explore attitudes towards welfare assessment. Participants (n = 48) from equestrian sport (n = 38) and animal welfare research (n = 10) attended a workshop that included welfare-related presentations and focus group sessions. The focus group sessions were recorded, anonymised and analysed using thematic analysis. Conflict between the demands of competition and the needs of the horse was identified as a key welfare challenge. Although the physical health of equine athletes is closely monitored, horses' psychological needs are sometimes overlooked. Participants recognised that improving competition practices may not be as impactful as improving the general management and training of horses. The term "quality of life" was considered preferable to "welfare", which had negative connotations. Participants appreciated the idea of incorporating formal welfare assessments into their training and competition plans but stated that existing tools are rarely used and are not deemed feasible for real-life conditions.

16.
Sci Adv ; 7(36): eabf7668, 2021 Sep 03.
Article in English | MEDLINE | ID: mdl-34516924

ABSTRACT

Peptides' hierarchical coassembly into nanostructures enables controllable fabrication of multicomponent biomaterials. In this work, we describe a computational and experimental approach to design pairs of charge-complementary peptides that selectively coassemble into ß-sheet nanofibers when mixed together but remain unassembled when isolated separately. The key advance is a peptide coassembly design (PepCAD) algorithm that searches for pairs of coassembling peptides. Six peptide pairs are identified from a pool of ~106 candidates via the PepCAD algorithm and then subjected to DMD/PRIME20 simulations to examine their co-/self-association kinetics. The five pairs that spontaneously aggregate in kinetic simulations selectively coassemble in biophysical experiments, with four forming ß-sheet nanofibers and one forming a stable nonfibrillar aggregate. Solid-state NMR, which is applied to characterize the coassembling pairs, suggests that the in silico peptides exhibit a higher degree of structural order than the previously reported CATCH(+/−) peptides.

17.
J Chem Phys ; 154(14): 144702, 2021 Apr 14.
Article in English | MEDLINE | ID: mdl-33858170

ABSTRACT

Adhesives that can stick to multiple surface types in underwater and high moisture conditions are critical for various applications such as marine coatings, sealants, and medical devices. The analysis of natural underwater adhesives shows that L-3,4-dihydroxyphenylalanine (DOPA) and functional amyloid nanostructures are key components that contribute to the adhesive powers of these natural glues. The combination of DOPA and amyloid-forming peptides into DOPA-amyloid(-forming peptide) conjugates provides a new approach to design generic underwater adhesives. However, it remains unclear how the DOPA monomers may interact with amyloid-forming peptides and how these interactions may influence the adhesive ability of the conjugates. In this paper, we investigate the behavior of DOPA monomers, (glycine-DOPA)3 chains, and a KLVFFAE and DOPA-glycine chain conjugate in aqueous environments using molecular simulations. The DOPA monomers do not aggregate significantly at concentrations lower than 1.0M. Simulations of (glycine-DOPA)3 chains in water were done to examine the intra-molecular interactions of the chain, wherein we found that there were unlikely to be interactions detrimental to the adhesion process. After combining the alternating DOPA-glycine chain with the amyloid-forming peptide KLVFFAE into a single chain conjugate, we then simulated the conjugate in water and saw the possibility of both intra-chain folding and no chain folding in the conjugate.

18.
J Phys Chem B ; 125(16): 4004-4015, 2021 04 29.
Article in English | MEDLINE | ID: mdl-33876641

ABSTRACT

Coassembling peptides offer an additional degree of freedom in the design of nanostructured biomaterials when compared to analogous self-assembling peptides. Yet, our understanding of how amino acid sequences encodes coassembled nanofiber structure is limited. Prior work on a charge-complementary pair, CATCH+ and CATCH- peptides, detected like-peptide nearest neighbors (CATCH+:CATCH+ and CATCH-:CATCH-) within coassembled ß-sheet nanofibers; these self-associated peptide pairs marked a departure from an "ideal" coassembled structure. In this work, we employ solid-state NMR, isotope-edited FTIR, and coarse-grained molecular dynamics simulations to evaluate the alignment of ß-strands within CATCH peptide nanofibers. Both experimental and computational results suggest that CATCH molecules coassemble into structurally heterogeneous nanofibers, which is consistent with our observations in another coassembling system, the King-Webb peptides. Within ß-sheet nanofibers, ß-strands were found to have nearest neighbors aligned in-register parallel, in-register antiparallel, and out-of-register. In comparison to the King-Webb peptides, CATCH nanofibers exhibit a greater degree of structural heterogeneity. By comparing the amino acid sequences of CATCH and King-Webb peptides, we can begin to unravel sequence-to-structure relationships, which may encode more precise coassembled ß-sheet nanostructures.


Subject(s)
Nanofibers , Amino Acid Sequence , Molecular Dynamics Simulation , Peptides , Protein Conformation, beta-Strand
19.
AIChE J ; 67(3): e17101, 2021 Mar.
Article in English | MEDLINE | ID: mdl-33776061

ABSTRACT

Determining the structure of the (oligomeric) intermediates that form during the self-assembly of amyloidogenic peptides is challenging because of their heterogeneous and dynamic nature. Thus, there is need for methodology to analyze the underlying molecular structure of these transient species. In this work, a combination of fluorescence quenching, photo-induced crosslinking (PIC) and molecular dynamics simulation was used to study the assembly of a synthetic amyloid-forming peptide, Aß16-22. A PIC amino acid containing a trifluormethyldiazirine (TFMD) group-Fmoc(TFMD)Phe-was incorporated into the sequence (Aß*16-22). Electrospray ionization ion-mobility spectrometry mass-spectrometry (ESI-IMS-MS) analysis of the PIC products confirmed that Aß*16-22 forms assemblies with the monomers arranged as anti-parallel, in-register ß-strands at all time points during the aggregation assay. The assembly process was also monitored separately using fluorescence quenching to profile the fibril assembly reaction. The molecular picture resulting from discontinuous molecule dynamics simulations showed that Aß16-22 assembles through a single-step nucleation into a ß-sheet fibril in agreement with these experimental observations. This study provides detailed structural insights into the Aß16-22 self-assembly processes, paving the way to explore the self-assembly mechanism of larger, more complex peptides, including those whose aggregation is responsible for human disease.

20.
Phys Chem Chem Phys ; 23(10): 5936-5944, 2021 Mar 18.
Article in English | MEDLINE | ID: mdl-33666204

ABSTRACT

Water + elastin-like polypeptides (ELPs) exhibit a transition temperature below which the chains transform from collapsed to expanded states, reminiscent of the cold denaturation of proteins. This conformational change coincides with liquid-liquid phase separation. A statistical-thermodynamics theory is used to model the fluid-phase behavior of ELPs in aqueous solution and to extrapolate the behavior at ambient conditions over a range of pressures. At low pressures, closed-loop liquid-liquid equilibrium phase behavior is found, which is consistent with that of other hydrogen-bonding solvent + polymer mixtures. At pressures evocative of deep-sea conditions, liquid-liquid immiscibility bounded by two lower critical solution temperatures (LCSTs) is predicted. As pressure is increased further, the system exhibits two separate regions of closed-loop of liquid-liquid equilibrium (LLE). The observation of bimodal LCSTs and two re-entrant LLE regions herald a new type of binary global phase diagram: Type XII. At high-ELP concentrations the predicted phase diagram resembles a protein pressure denaturation diagram; possible "molten-globule"-like states are observed at low concentration.


Subject(s)
Elastin/chemistry , Peptides/chemistry , Computer Simulation , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Models, Molecular , Phase Transition , Solvents/chemistry , Thermodynamics , Transition Temperature
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