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Probabilistic genotype-phenotype maps reveal mutational robustness of RNA folding, spin glasses, and quantum circuits

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Physical Review Research 2025年第1期7卷 013118-013118页

作者： Anna Sappington Vaibhav Mohanty Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Harvard-MIT Program in Health Sciences and Technology Harvard Medical School Boston Massachusetts 02115 USA and Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Harvard/MIT MD-PhD Program Harvard Medical School Boston Massachusetts 02115 USA and Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Department of Chemistry and Chemical Biology Harvard University Cambridge Massachusetts 02138 USA

Recent studies of genotype-phenotype maps have reported universally enhanced phenotypic robustness to genotype mutations, a feature essential to evolution. Virtually all of these studies make a simplifying assumption that each genotype—represented as a sequence—maps deterministically to a single phenotype, such as a discrete structure. Here we introduce probabilistic genotype-phenotype (PrGP) maps, where each genotype maps to a vector of phenotype probabilities, as a more realistic and universal language for investigating robustness in a variety of physical, biological, and computational systems. We study three model systems to show that PrGP maps offer a generalized framework which can handle uncertainty emerging from various physical sources: (1) thermal fluctuation in RNA folding, (2) external field disorder in the spin-glass ground state search problem, and (3) superposition and entanglement in quantum circuits, which are realized experimentally on IBM quantum computers. In all three cases, we observe a biphasic robustness scaling which is enhanced relative to random expectation for more frequent phenotypes and approaches random expectation for less frequent phenotypes. We derive an analytical theory for the behavior of PrGP robustness, and we demonstrate that the theory is highly predictive of empirical robustness.

关键词： Quantum computers

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Directed discovery of high-loading nanoaggregates enabled by drug-matched oligo-peptide excipients

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Chem 2025年

作者： Berisha, Naxhije Farahpour, Atena Ramakrishnan, Maithreyi Chen, Chen McPhee, Scott A. Wang, Tong Li, Tai-De Hema, Kuntrapakam Panagiotakopoulou, Magdalini Athiyarath, Vignesh Coste, Maeva Marciano, Yaron Sherman, Emmet Ulijn, Rein V. Heller, Daniel A. Nanoscience Initiative Advanced Science Research Center CUNY Graduate Center City University of New York New York 10031 NY United States Department of Chemistry and Biochemistry Hunter College City University of New York New York 10065 NY United States PhD Program in Chemistry CUNY Graduate Center City University of New York New York 10016 NY United States Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New York 10065 NY United States Tri-Institutional PhD Program in Chemical Biology Memorial Sloan Kettering Cancer Center New York 10065 NY United States Department of Physics City College of New York City University of New York New York 10031 NY United States Department of Chemistry Brooklyn College City University of New York 2900 Bedford Avenue Brooklyn 11210 NY United States PhD Program in Biochemistry CUNY Graduate Center City University of New York New York 10016 NY United States Weill Cornell Medicine Cornell University New York 10065 NY United States

Nanoparticles can improve drug pharmacokinetics, but low loading efficiencies can limit treatment efficacy. Drug-aggregation-based nanoparticles have demonstrated improved loadings of up to 90%, but few excipients facilitate efficient co-assembly. We investigated peptides as designer excipients because of their diverse chemical space and inherent biodegradability. We designed pentapeptide scaffolds to mimic the structure of known indocyanine excipients by modulating aromaticity, rigidity, and charge. We screened 184 formulations by using diverse drug cargoes. We found drug-peptide combinations that formed nanoparticles with up to 98% drug loading. Molecular dynamics simulations and mass spectrometry analysis demonstrated that tryptophan-drug interactions and solvent exposure of charged amino acid residues drove the formation of core-shell structures. Peptide-drug formulations containing the JAK2/FLT3 inhibitor lestaurtinib were investigated in acute myeloid leukemia models, resulting in enhanced anti-tumor efficacy. This work found that oligopeptides can be designed to efficiently co-assemble with therapeutic cargoes to result in high-loading nanoparticles that improve anti-tumor efficacy. © 2024

关键词： co-assembly directed discovery drug delivery excipient nanocarrier design nanoparticle oligopeptides SDG3: Good health and well-being

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Four Examples of Unimolecular Electrical Rectifiers

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Electrochemical Society Interface 2004年第1期13卷 40-44页

作者： Metzger, Robert M. Department of Chemistry Materials Science PhD Program United States Department of Chemistry University of Mississippi United States

The unimolecular electronics (UE) aims to produce molecular electronic devices at 1-2 nm scale to meet the needs of integrated circuits. The UE is advanced by measuring electrical conductivity of single molecules or Langmuir-Blodgett (LB) monolayers. A single molecule is touched by scanning tunneling microscopy (STM) tip, conducting-tip atomic force microscopy (AFM) tip or between two Au tips are measured in parallel by making electrical contacts to sandwiches of organic monolayers. The metal | organic | metal sandwiches are prepared and measured without destroying organic layer.

关键词： Electric rectifiers

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Nitro-driven electrophilicity: A combined HPLC and computational study of para-nitrophenylethylamine and its impurities

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Journal of Liquid Chromatography and Related Technologies 2025年

作者： Sharma, Sanjay Kumar Sultana, Sayeeda Sharma, Vivek Yañez, Osvaldo Cantero-López, Plinio Department of Chemistry St. Peter’s Institute of Higher Education and Research Tamil Nadu Chennai India Research and Development Zenfold Sustainable Technologies Pvt Ltd Karnataka Bangalore India Department of Chemistry Faculty of Technology and Sciences Lovely Professional University Punjab Phagwara India Facultad de Ingeniería y Negocios Universidad de Las Américas Santiago Chile Facultad de Ciencias Exactas Departamento de Ciencias Químicas Universidad Andres Bello Viña del Mar Chile Facultad de Ciencias Exactas Universidad Andres Bello Santiago Chile PhD program in Molecular Physical Chemistry Facultad de Ciencias Exactas Universidad Andres Bello Santiago Chile

The manuscript deals with the development, validation, and theoretical chemistry behind a reverse-phase HPLC methodology needed to separate, identify, and evaluate the content of 4-nitrophenyl ethylamine (4-NPA) and its associated impurities (i.e., 2-NPA, 3-NPA, 2-PEA, and acetamide impurity). The developed HPLC method was found to be specific, linear, precise, repeatable, accurate, and robust. This method can be used to assess the quality of 4-NPA sample for the quantification of 2-NPA, 3-NPA, 2-PEA, acetamide impurity. The purpose of this research is for separation and quantification of positional isomers, which is mandatory during the analysis of 4-NPA samples to avoid further formation of analogues derivative of 2-NPA and 3-NPA intermediate and drug substances. Computational studies demonstrated that nitro substitution, regardless of its position, enhances the electron-accepting capacity of the molecule and its overall reactivity, while decreasing its stability. The persistent trend of enhanced electrophilicity and electron-accepting characteristics (2-PEA © 2025 Taylor & Francis Group, LLC.

关键词： High pressure liquid chromatography

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Unveiling the potential of bacterial keratinase with antiacne drugs for cosmeceutical applications: an in silico evaluation

Journal of Umm Al-Qura University for Applied Sciences

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Journal of Umm Al-Qura University for Applied Sciences 2025年 1-24页

作者： Gaur, Peehoo Polipalli, Yuvaraj Bandhu, Xena Chakravarty, Suhani Banerjee, Srijan Meza, Cynthia Suravajhala, Renuka Sarkar, Shrabana Banerjee, Aparna India International School (IIS) Rajasthan Jaipur India Dr. Durgabhai Deshmukh Senior Secondary School DDU Marg New Delhi India KC Public School Akhnoor Road J&K Jammu India Ankur Senior Secondary School Chandigarh Panjab University Campus Sector 14 Chandigarh India PhD Program in Science R & D Bioactive Products Department Chemistry Institute of Natural Resources University of Talca Talca Chile Doctorado en Biotecnología Traslacional (DBT) Facultad de Ciencias Agrarias y Forestales Universidad Católica del Maule Talca Chile *** Hyderabad India Amrita School of Biotechnology Amrita Vishwa Vidyapeetham Kerala Amritapuri India Functional Polysaccharides Research Group Instituto de Ciencias Aplicadas Facultad de Ingeniería Universidad Autónoma de Chile Talca Chile

The keratinase serves as a catalyst with potential application in various industries, including textiles, leather, pharmaceuticals, cosmetics, and biotechnological applications. Previous studies have predominantly focused on fungal keratinase;however, our present work focuses on bacterial keratinase only. The novelty of using bacterial keratinase over fungal keratinase is because of its faster enzymatic activity, broader substrate specificity, increased stability and cost-effective production, making it efficient and adaptable for industrial applications. However, our present research investigates bacterial keratinase through in silico structural (physicochemical properties, primary, secondary, and tertiary structures) as well as functional analyses (protein–protein interaction networks, subcellular localization, and domain/motif presence), coupled with molecular docking against standard anti-acne drugs in use (adapalene, erythromycin, tretinoin, isotretinoin, and benzoyl peroxide). In this study, two bacterial keratinases, one from mesophilic Pseudomonas aeruginosa (6FZX) and another from thermophilic Meiothermus taiwanensis WR-220 (5WSL) have been studied to demonstrate comparative structural stability and functional activity. These enzymes are intracellular, facilitating proteolysis with metalloendopeptidase activity. Notably, keratinase exhibited a strong binding affinity for adapalene (binding energies of − 8.5 kcal/mol and − 9.6 kcal/mol for 5WSL and 6FZX, respectively) and lowest affinity to erythromycin (binding energy − 6.4 kcal/mol and − 5.9 kcal/mol for 5WSL and 6FZX respectively) among other studied anti-acne drugs like, tretinoin, isotretinoin, and benzoyl peroxide. In the case of de novo designing of anti-acne compounds, enhanced binding affinities are the key factor for selection of potential components. Our in silico analyses indicate that thermophilic keratinase displays better structural stability and functionality, particularly under high pH and h

关键词： Bacteria Cosmeceuticals Functional analyses Keratinase Molecular docking Structural analyses

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BPS2025 - Analysis of the steady states of systems of dynamic microtubules: Polymer length distribution steady state

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Biophysical Journal 2025年第3期124卷 139a-139a页

作者： Alexander W. Simmons Sayandeepa Raha Theodore N. Berente Holly V. Goodson Department of Chemistry and Biochemistry University of Notre Dame Notre Dame IN USA Biophysics PhD Program University of Notre Dame Notre Dame IN USA Integrated Biomedical Sciences PhD Program University of Notre Dame Notre Dame IN USA QuarkNet University of Notre Dame Notre Dame IN USA St. Joseph High School South Bend IN USA

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Variations in kinase and effector signaling logic in a bacterial two component signaling network

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Journal of Biological chemistry 2025年第6期301卷

作者： Danielle Swingle Leah Epstein Ramisha Aymon Eta A. Isiorho Rinat R. Abzalimov Denize C. Favaro Kevin H. Gardner Structural Biology Initiative CUNY Advanced Science Research Center New York New York USA PhD. Program in Biochemistry The Graduate Center – City University of New York New York New York USA Department of Chemistry and Biochemistry City College of New York New York New York USA PhD. Programs in Biochemistry Biology and Chemistry The Graduate Center – City University of New York New York New York USA

The general stress response (GSR) protects bacteria from a wide range of stressors. In Alphaproteobacteria , GSR activation is coordinated by HWE/HisKA2 family histidine kinases (HKs), which can exhibit noncanonical structure and function. For example, while most light-oxygen-voltage sensor-containing HKs are light-activated dimers, the Rubellimicrobium thermophilum RT-HK has inverted “dark on, light off” signaling logic with a tunable monomer/dimer equilibrium. Here, we further investigate these atypical behaviors of RT-HK and characterize its downstream signaling network. Using hydrogen-deuterium exchange mass spectrometry, we find that RT-HK uses a signal transduction mechanism similar to light-activated systems, despite its inverted logic. Mutagenesis reveals that RT-HK autophosphorylates in trans , with changes to the Jα helix linking sensor and kinase domains affecting autophosphorylation levels. Exploring downstream effects of RT-HK, we identified two GSR genetic regions, each encoding a copy of the central regulator PhyR. In vitro measurements of phosphotransfer from RT-HK to the two putative PhyRs revealed that RT-HK signals only to one and does so at an increased intensity in the dark, consistent with its reversed logic. X-ray crystal structures of both PhyRs revealed a substantial shift within the receiver domain of one, suggesting a basis for RT-HK specificity. We probed further down the pathway using nuclear magnetic resonance to determine that the single NepR homolog interacts with both unphosphorylated PhyRs, and this interaction is decoupled from activation in one PhyR. This work expands our understanding of HWE/HisKA2 family signal transduction, revealing marked variations from signaling mechanisms previously identified in other GSR networks.

关键词： histidine kinase bacterial signal transduction stress response protein structure two-component system response regulators hydrogen exchange mass spectrometry CA catalytic ATP-binding DHp dimerization histidine phosphotransfer GSR general stress response HDX-MS hydrogen-deuterium exchange mass spectrometry HK histidine kinase LOV light-oxygen-voltage NMR nuclear magnetic resonance REC receiver domain RR response regulator SL sigma-like domain TROSY transverse relaxation-optimized spectroscopy

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Bio-based adsorbents of cellulose nanofibrils: An experimental and theoretical investigation of methyl orange removal

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Journal of Molecular Liquids 2025年 427卷

作者： Oyarce, Estefanía Cantero-López, Plinio Roa, Karina Boulett, Andrés Yáñez, Osvaldo Pizarro, Guadalupe Sánchez, Julio Departamento de Química Orgánica Facultad de Química y de Farmacia Pontificia Universidad Católica de Chile Santiago Chile Santiago Chile Universidad Andres Bello Facultad de Ciencias Exactas Departamento de Ciencias Químicas Viña del Mar2531015 Chile Facultad de Ciencias Exactas Universidad Andres Bello Santiago8370186 Chile PhD Program in Molecular Physical Chemistry Facultad de Ciencias Exactas Universidad Andres Bello Santiago8370146 Chile Núcleo de Investigación en Data Science Facultad de Ingeniería y Negocios Universidad de Las Américas Santiago7500975 Chile Chile

The removal of dyes from water is an area of great relevance worldwide, and new technologies and materials are therefore continuously investigated. In this context, bioadsorbents based on cellulose nanofibrils (CNF) and poly(vinylbenzyl)trimethylammonium chloride (PClVBTA) were developed to study the adsorption of methyl orange (MO) dye. Radical polymerization enabled the successful creation of these adsorbents, with CNF modifying the physicochemical properties of the base material, as evidenced by Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and dynamic compression tests. The adsorption capacities improved with increasing CNF content, reaching an experimental adsorption capacity of 579 mg g−1 for MO when 1.00 wt% CNF was used. The experimental data were fitted to the Elovich kinetic and Langmuir isothermal models, and the thermodynamic parameters indicated that the adsorption is favorable. The adsorption of MO was confirmed by FT-IR, BET isotherms, and energy dispersive spectroscopy (EDS) analysis. Interfering salts in the aqueous medium did not affect significantly, and the adsorbent material was reusable for up to five cycles. Theoretical studies highlighted π interactions and hydrogen bonding, demonstrating that the incorporation of CNF improves the sustainability and performance of the adsorbents in water purification. © 2025 Elsevier B.V.

关键词： Energy dispersive spectroscopy

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Potential vibrational modes tied to diffuse interstellar bands

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Monthly Notices of the Royal Astronomical Society 2025年第4期539卷 3489-3492页

作者： Majaess, Daniel Seuret, Halis Harriott, Tina A. Morera-Boado, Cercis Sullivan, Ailish D. Massa, Lou Matta, Chérif F. Department of Chemistry and Physics Mount Saint Vincent University HalifaxNSB3M2J6 Canada Centro de Investigaciones Químicas IICBA Universidad Autónoma del Estado de Morelos Morelos Cuernavaca62209 Mexico Department of Mathematics and Statistics Mount Saint Vincent University HalifaxNSB3M2J6 Canada IXM-Cátedra Conahcyt-Centro de Investigaciones Químicas IICBA Universidad Autónoma del Estado de Morelos Morelos Cuernavaca62209 Mexico Hunter College the PhD Program of the Graduate Center City University of New York New York10016 United States Department of Chemistry Saint Mary’s University HalifaxNSB3H3C3 Canada Département de Chimie Université Laval QuébecG1V0A6 Canada Department of Chemistry Dalhousie University HalifaxNSB3H4J3 Canada

Potential vibrational modes associated with diffuse interstellar bands (DIBs) could be discerned by examining energy differences between correlated DIBs. Consequently, ≈ 103 higher correlated DIB pairs (r − σr ≥ 0.8, ≥ 12 sightlines) were extracted from the Apache Point Observatory DIB catalogue, and their energy spacings computed. In this first macro exploratory step, a histogram possibly reveals chemical bond signatures of C≡C, C≡N, S−H, C−O, C=O, Si−H, N−H, C−H (aliphatic), C...C (in-ring), and aromatics (C−H stretch, C...C in-ring, oop C−H bending, overtones and combinations). Continued research is required to (in)validate the histogram approach, mitigate noise, scrutinize maxima, break degeneracies, and converge upon an optimal framework. © 2025 The Author(s)

关键词： Bond strength (chemical)

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Teaching Green chemistry Through Student-Generated Open Educational Resources

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Journal of College Science Teaching 2023年第4期52卷 3-5页

作者： Grieger, Krystal Leontyev, Alexey Department of Chemistry and Biochemistry North Dakota State University in Fargo ND United States Department of Chemistry and Biochemistry and Discipline-Based Education Research PhD Program North Dakota State University Fargo ND United States

This article describes the implementation of a student-generated open educational resource project into a majors ’ organic chemistry laboratory. This scaffolded semester-long project was organized into six phases and designed to promote the goals of teaching students about both green chemistry and real-life applications of the reactions covered in the course while simultaneously creating open educational resources for future students. A project-based learning approach was utilized to promote student engagement, especially during remote instruction. To further promote engagement, multiple opportunities for peer feedback were provided using web-based software that supports anonymous feedback. The effect of the project on cognitive learning gains and student perceptions was assessed and is reported. Overall, positive learning gains on green chemistry knowledge and skills were observed, and most students viewed the project favorably. © 2023 National Science Teaching Association.

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