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1. Remote controlled optical manipulation of bimetallic nanoparticle catalysts using peptides

   https://doi.org/10.1039/D1CY00189B  

   Lawrence, Randy L.; Olagunju, Mary O.; Liu, Yang; Mahalingam, Krishnamurthy; Slocik, Joseph M.; Naik, Rajesh R.; Frenkel, Anatoly I.; Knecht, Marc R. (April 2021, Catalysis Science & Technology)

   null (Ed.)

   Bimetallic nanoparticles remain a promising avenue to achieve highly reactive catalysts. In this contribution, we demonstrate the use of a photoswitchable peptide for the production of PdAu bimetallic nanoparticles at a variety of Pd : Au ratios. Using this peptide, the biomolecular overlayer structure can be switched between two different conformations ( cis vs. trans ) via light irradiation, thus accessing two different surface structures. The composition and arrangement of the materials was fully characterized, including atomic-level analyses, after which the reactivity of the bimetallic materials was explored using the reduction of 4-nitrophenol as a model system. Using these materials, it was demonstrated that the reactivity was maximized for the particles prepared at a Pd : Au ratio of 1 : 3 and with the peptide in the cis conformation. Such results present routes to a new generation of catalysts that could be remotely activated for on/off reactivity as a function of the ligand overlayer conformation. 

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2. An Unbound Proline-Rich Signaling Peptide Frequently Samples Cis Conformations in Gaussian Accelerated Molecular Dynamics Simulations

   https://doi.org/10.3389/fmolb.2021.734169  

   Alcantara, Juan; Stix, Robyn; Huang, Katherine; Connor, Acadia; East, Ray; Jaramillo-Martinez, Valeria; Stollar, Elliott J.; Ball, K. Aurelia (November 2021, Frontiers in Molecular Biosciences)

   Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the cis state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in cis , a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the cis conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the cis and trans states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline cis and trans states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in cis , leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in trans . The ensemble containing cis prolines also matches more closely to in vitro circular dichroism data than the all- trans ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with in vitro data. 

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3. Quantifying how the cis / trans ratio of N , N -dimethyl-3,5-dimethylpiperidinium hydroxide impacts the growth kinetics, composition and local structure of SSZ-39

   https://doi.org/10.1039/d4ra08620a  

   Cui, Zheng; Umhey, Charles E; Ukagha, Onyinyechukwu C; Ogunleye, Motunrayo; McEwen, Jean-Sabin; Shantz, Daniel F (March 2025, RSC Advances)

   This work integrates experiments and computational methods to quantify how the cis/trans ratio of the OSDA used in SSZ-39 synthesis impacts the crystallization kinetics, material properties, and final product composition. The crystallization kinetics increase by 30% when increasing the trans isomer content from 14% to 80%. Per prior work, in all cases based on the synthesis gel composition and product yield aluminum is the limiting reagent, and the absence of any amorphous material detected in the time resolved PXRD studies leads us to conclude that FAU dissolution is the rate limiting step in the formation of SSZ-39 in this synthesis protocol. The TGA and NMR results suggest that the trans isomer of OSDA is selectively incorporated into the product. The NMR binding studies, and corresponding DFT-based results show that the trans isomer binds to FAU more strongly than the cis isomer, providing one possible explanation for this enhancement in kinetics and preferential uptake of the trans isomer. The EDS analysis indicates that the Si/Al ratios are between 7.7 and 8.6 at low and high trans OSDA content, indicating zeolite composition is mildly sensitive to the trans isomer content. EDS results show this decrease in aluminum content leads to a corresponding decrease in sodium uptake. DFT-based calculations confirm OSDA–sodium interactions cannot explain any decrease in sodium uptake, reinforcing lower aluminum content as the cause of lower sodium uptake. Preliminary cobalt titration experiments show a surprisingly low cobalt uptake but also show a clear dependence of the cobalt uptake on the solution pH. 

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4. Function and solution structure of the Arabidopsis thaliana RALF8 peptide

   https://doi.org/10.1002/pro.3628  

   Frederick, Ronnie O.; Haruta, Miyoshi; Tonelli, Marco; Lee, Woonghee; Cornilescu, Gabriel; Cornilescu, Claudia C.; Sussman, Michael R.; Markley, John L. (May 2019, Protein Science)

   Abstract We report the recombinant preparation fromEscherichia colicells of samples of two closely related, small, secreted cysteine‐rich plant peptides: rapid alkalinization factor 1 (RALF1) and rapid alkalinization factor 8 (RALF8). Purified samples of the native sequence of RALF8 exhibited well‐resolved nuclear magnetic resonance (NMR) spectra and also biological activity through interaction with a plant receptor kinase, cytoplasmic calcium mobilization, andin vivoroot growth suppression. By contrast, RALF1 could only be isolated from inclusion bodies as a construct containing an N‐terminal His‐tag; its poorly resolved NMR spectrum was indicative of aggregation. We prepared samples of the RALF8 peptide labeled with¹⁵N and¹³C for NMR analysis and obtained near complete¹H,¹³C, and¹⁵N NMR assignments; determined the disulfide pairing of its four cysteine residues; and examined its solution structure. RALF8 is mostly disordered except for the two loops spanned by each of its two disulfide bridges. 

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5. Ozonolysis Dissociation Kinetics for the Relative Quantification of Geometrical Phosphatidylcholine Isomers

   https://doi.org/10.1021/acs.analchem.5c00670  

   Scoggins_IV, Troy R; Guo, Yingchan; Zerebinski, Paul; Prentice, Boone M (June 2025, Analytical Chemistry)

   The structural diversity of lipids presents significant challenges for accurate identification and characterization, ne-cessitating advanced analytical tools. Among these challenges is the differentiation between cis and trans isomers of lipids, which differ only by the geometry of a carbon-carbon double bond. This study employs ozonolysis kinetics to distinguish these isomers based on the reactivity of their gas phase ions with ozone. To achieve precise differentia-tion, it is essential to use an ion adduct that enhances reactivity, thereby improving the sensitivity of the kinetic assays. We evaluated various ion types, including protonated lipids as well as lipids cationized with lithium, sodium, and potassium, using a modified quadrupole ion trap mass spectrometer. Our results demonstrate that lithium-adducted lipids exhibit the highest reaction efficiency and greatest sensitivity for distinguishing between cis and trans isomers. Subsequent analysis of cis and trans isomer mixtures of PC 18:1/18:1 (Δ9), PC 16:1/16:1 (Δ9), and PC 14:1/14:1 (Δ9) confirmed the method's robustness. 

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