Article
Biochemistry & Molecular Biology
Sathish Kumar Marimuthu, Krishnanand Nagarajan, Sathish Kumar Perumal, Selvamani Palanisamy, Latha Subbiah
Summary: Host defense peptides or antimicrobial peptides (AMPs) are short sequences of amino acids with positive or negative charges that exhibit broad-spectrum antibacterial, antiviral, and antifungal activity. AMPs rich in tryptophan, arginine, and proline are considered promising sources for the development of next-generation antibiotics. This study analyzed and classified 2924 AMPs based on their amino acid sequences and investigated their structures and stability using modeling and simulations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Bence Feher, Levena Gascoigne, Sanne N. Giezen, Ilja K. Voets
Summary: Membrane fusion plays a vital role in biological processes such as cellular uptake, cell communication, and RNA delivery. This study focuses on the role of coiled-coil (CC) peptides, particularly the E-K complex, in membrane fusion. By substituting lysine amino acids with arginine at different positions in the peptide sequence, the researchers found that increasing the amount of arginine enhances the peptide's affinity to the membrane. Molecular dynamics simulations and coarse-grained simulations also showed that the interaction between the peptides and the membrane triggers increased membrane curvature without disrupting lipid packing. Furthermore, all modified peptides retained the ability to form CC complexes with E peptides. The findings suggest that the positioning of arginine is critical when designing CC fusion peptides. Peptides with arginines located at the N-terminus exhibit greater affinity to the lipid membrane. Introducing arginine into CC peptide sequences can enhance binding affinity to the membrane and may lead to more effective CC fusion peptides than the E-K complexes.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Multidisciplinary Sciences
Meghan H. Murray, Aurore Cecile Valfort, Thomas Koelblen, Celine Ronin, Fabrice Ciesielski, Arindam Chatterjee, Giri Babu Veerakanellore, Bahaa Elgendy, John K. Walker, Lamees Hegazy, Thomas P. Burris
Summary: The nuclear receptor REV-ERB plays a crucial role in physiological processes and is stimulated by heme. However, the binding and regulatory mechanisms of synthetic agonists for REV-ERB are still unknown.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Flavio Costa, Carlo Guardiani, Alberto Giacomello
Summary: The study suggests two distinct pathways as the possible molecular basis of inactivation mechanism in the K(v)1.2 channel, consistent with earlier mutational studies and known mutations involved in neuronal channelopathies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Applied
Miguel Riopedre-Fernandez, Denys Biriukov, Martin Dracinsky, Hector Martinez-Seara
Summary: This study investigates the molecular motifs of hyaluronan-peptide interactions using NMR and molecular dynamics simulations. The results show that arginine-rich peptides have the strongest binding to hyaluronan, followed by lysine. Molecular simulations reveal an extended but significant interaction region, especially for arginine, which explains the enhanced binding between hyaluronan and positively charged arginine-rich proteins.
CARBOHYDRATE POLYMERS
(2024)
Article
Genetics & Heredity
Yi-Chun Wang, Shang-Hsuan Huang, Chien-Ping Chang, Chuan Li
Summary: Researchers developed a GAR motif finder (GMF) program to analyze the characteristics of the long GAR domains in FBL and other nucleolar proteins. The program can illustrate the similarities and differences between these domains and other proteins containing RG/RGG repeats, and classify the long GAR motifs based on their putative correlation with protein/RNA interactions and liquid-liquid phase separation.
Article
Chemistry, Physical
Emmanuelle Bignon, Angelo Spinello, Tom Miclot, Luisa D'Anna, Cosimo Ducani, Stephanie Grandemange, Giampaolo Barone, Antonio Monari, Alessio Terenzi
Summary: This article investigates the interplay among three G4 sequences in the c-KIT proto-oncogene promoter and finds that their structural linkage favors the formation of a parallel structure for WSP. Using molecular dynamics simulations and enhanced sampling methods, they provide the first computationally resolved structure of a well-organized G4 cluster in the promoter of a crucial gene involved in cancer development. The study suggests that neighboring G4s influence their mutual three-dimensional arrangement and provide a powerful tool for predicting and interpreting complex DNA structures, which can be used as a starting point for drug discovery.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Yu Zheng, Perla B. Balbuena
Summary: This study investigates the reactivities of three substances in the electrolyte solution, finding that LiFSI and TFEO have high reduction activity, while DME shows good stability with excess electrons. Most relevant reactions are thermodynamically favorable with low activation barriers.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Review
Plant Sciences
Zi-Chang Jia, Debatosh Das, Youjun Zhang, Alisdair R. Fernie, Ying-Gao Liu, Moxian Chen, Jianhua Zhang
Summary: Serine/arginine-rich (SR) proteins participate in RNA processing and maintain plant growth and stress responses through interactions with precursor mRNAs or other splicing factors. SR proteins are crucial for alternative splicing and play essential roles in the composition and alternative splicing of precursor mRNAs. However, their evolutionary trajectory, molecular function, and regulatory network in plants are still largely unknown compared to their animal counterparts. This article reviews the current understanding of the SR protein family in eukaryotes and proposes potential key research priorities for future functional studies.
Article
Multidisciplinary Sciences
Fabian Heide, Matthew McDougall, Candice Harder-Viddal, Roy Roshko, David Davidson, Jiandong Wu, Camila Aprosoff, Aniel Moya-Torres, Francis Lin, Jorg Stetefeld
Summary: Boron neutron capture therapy (BNCT) is a therapeutic process that utilizes Boron-10 and low energy neutrons to eliminate targeted cells, primarily used for head and neck carcinomas. A proteinaceous nanotube drug delivery system has been investigated as a potential candidate for delivering Boron-10 into cancer cells, showing promising results in experimental studies.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Baosheng Li, Qing Cai, Zixuan Wang, Shuwei Qiao, Yanzhen Ou, Rui Ma, Chuanfu Luo, Weiyan Meng
Summary: This study investigates the effects of alpha-amylase and D-arginine on disassembling Actinomyces viscosus biofilm. It was found that D-arginine enhances the disassembly effects of alpha-amylase on A. viscosus biofilm by potentiating the catalytic triad and stabilizing the calcium-binding regions. This provides a novel strategy for the decontamination of biofilm on implant surfaces.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Evan van Aalst, Jotham Koneri, Benjamin J. Wylie
Summary: Investigations into cholesterol binding sites in CCR3 have revealed the presence of multiple binding sites containing Cholesterol Recognition/Interaction Amino Acid Consensus motif (CRAC) and its inversion CARC motifs, with a particular site in TM1 and TM7 emerging as a candidate for future research based on cholesterol residency time and conservation in other chemokine receptors. These cholesterol binding sites may provide insights into cholesterol regulation mechanisms in the subfamily of Class A GPCRs.
Article
Polymer Science
Luis F. Pacios, Joseph Arguelles, Cheryl Y. Hayashi, Gustavo V. Guinea, Manuel Elices, Jose Perez-Rigueiro
Summary: This study used molecular dynamics to simulate the behavior of two polyglycine-rich fragments representing major ampullate gland spidroins (MaSp) 1 and 2 types in a water-saturated environment. It was found that the fragment from MaSp2 exhibited significantly higher recovery force compared to the fragment from MaSp1 when subjected to force.
Article
Biophysics
Ming Yuan, Jiaqi Lian, Xiaoning Han, Jing Wen, Jingyu Gao, Liping Wang, Feng Zhang
Summary: The molecule-like electronic structure of gold nanoclusters provides them with the fascinating property of fluorescence, making them highly promising for biomedical applications. In this study, tyrosine-containing peptide motifs were designed as reducing agents and protecting ligands to synthesize P-AuNCs in a one-step reaction, which allowed for real-time monitoring of the fluorescence evolution. The synthesized P-AuNCs exhibited a quantum yield of approximately 18% and demonstrated excellent performance in temperature and metal ion sensing, as well as cell labeling and imaging. This study presents a useful one-step synthesis strategy for screening peptide motifs to modulate the optical properties of peptide-containing hybrid nanomaterials in real-time.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Laszlo Temleitner, Takanori Hattori, Jun Abe, Yoichi Nakajima, Laszlo Pusztai
Summary: Total scattering structure factors of per-deuterated methanol and heavy water have been determined as a function of pressure using neutron diffraction, with molecular dynamics simulations providing further insights into the changes in local intermolecular structure caused by pressure variations. The shifts in peak positions due to increasing pressure were qualitatively reproduced by simulations, highlighting the importance of repulsive forces between neighboring molecules in these hydrogen-bonded liquid mixtures. Differences in pressure-dependent structures between water-rich and methanol-rich composition regions were also revealed through simulated structures analysis.
Article
Biotechnology & Applied Microbiology
Sandra M. Tallent, Jennifer M. Hait, Ann M. Knolhoff, Reginald W. Bennett, Thomas S. Hammack, Timothy R. Croley
JOURNAL OF FOOD SAFETY
(2017)
Article
Chemistry, Medicinal
Spencer S. Ericksen, Haozhen Wu, Huikun Zhang, Lauren A. Michael, Michael A. Newton, F. Michael Hoffmann, Scott A. Wildman
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2017)
Article
Chemistry, Multidisciplinary
Gao-Juan Cao, Christine M. Fisher, Xiumei Jiang, Yu Chong, Hui Zhang, Hongyu Guo, Qian Zhang, Jiwen Zheng, Ann M. Knolhoff, Timothy R. Croley, Jun-Jie Yin
Article
Chemistry, Analytical
Ann M. Knolhoff, Caitlin N. Kneapler, Timothy R. Croley
ANALYTICA CHIMICA ACTA
(2019)
Editorial Material
Chemistry, Medicinal
Giulia Palermo, Kira A. Armacost, Maria C. Nagan
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2019)
Review
Chemistry, Physical
Maria C. Nagan
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2020)
Article
Chemistry, Analytical
Ann M. Knolhoff, Jacob H. Premo, Christine M. Fisher
Summary: This study developed a proposed nontargeted standard/quality control mixture for NTA and SSA applications, consisting of 89 compounds. The utility of the standard mixture was evaluated in the authors' own workflows, identifying areas for improvement such as hydrophilic compound detection and molecular formula generation for compounds containing fluorine.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Applied
Ann M. Knolhoff, Christine M. Fisher
Summary: The study found that non-targeted analyses using LC/HR-MS can generate information-rich data sets, but data mining can be labor intensive. Different approaches were examined to reduce the number of compounds needing further investigation, with the use of inherent sample variability to build in-house databases for data reduction. Differential analysis was effective for single ingredient foods, while a combination of approaches was necessary for greater sample complexity.
Article
Chemistry, Analytical
Katherine T. Peter, Allison L. Phillips, Ann M. Knolhoff, Piero R. Gardinali, Carlos A. Manzano, Kelsey E. Miller, Manuel Pristner, Lyne Sabourin, Mark W. Sumarah, Benedikt Warth, Jon R. Sobus
Summary: Non-targeted analysis (NTA) workflows using mass spectrometry are becoming increasingly popular in various disciplines, but there is still a lack of universally accepted reporting standards. To address this issue, researchers have developed the NTA Study Reporting Tool (SRT), which has been shown to be effective in guiding study design, manuscript writing, and evaluating NTA reporting quality through analysis of published articles.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Benjamin J. Place, Elin M. Ulrich, Jonathan K. Challis, Alex Chao, Bowen Du, Kristin Favela, Yong-Lai Feng, Christine M. Fisher, Piero Gardinali, Alan Hood, Ann M. Knolhoff, Andrew D. McEachran, Sara L. Nason, Seth R. Newton, Brian Ng, Jamie Nunez, Katherine T. Peter, Allison L. Phillips, Natalia Quinete, Ryan Renslow, Jon R. Sobus, Eric M. Sussman, Benedikt Warth, Samanthi Wickramasekara, Antony J. Williams
Summary: Non-targeted analysis (NTA) is a rapidly evolving set of mass spectrometry techniques aimed at characterizing complex samples' chemical composition, identifying unknown compounds, and classifying samples. Recent advances are due to improved instrumentation and accessible data analysis tools, with a growing need for community-wide method reporting guidelines. This has led to the formation of the Benchmarking and Publications for Non-Targeted Analysis Working Group (BP4NTA) to address challenges and establish consensus in NTA-related terms and reporting practices.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Vinay Maddula, Nathalia S. Holtzman, Maria C. Nagan, Susan A. Rotenberg
Summary: This study found that protein kinase C-mediated phosphorylation of alpha-tubulin at a specific site can stimulate microtubule polymerization. Molecular simulations revealed that the phosphomimetic variant S165D alters the spatial relationship between alpha:Glu254 and beta:GTP, thereby slowing GTP hydrolysis and promoting the formation of GTP caps. Cellular experiments confirmed these findings.
Article
Chemistry, Medicinal
Kelly Anderson, Sarah Arradondo, K. Aurelia Ball, Chrystal Bruce, Maria A. Gomez, Kedan He, Heidi Hendrickson, Lindsey Madison, Ashley Ringer McDonald, Maria C. Nagan, Caitlin E. Scott, Patricia Soto, Aime'e Tomlinson, Mychel Varner, Carol Parish
Summary: The Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) has been supporting faculty and students for over 20 years, providing computational resources, networking opportunities, and professional support. The consortium consists of 38 faculty (42% women) at 34 institutions, who have trained almost 900 undergraduate students, with the majority being women and students of color. MERCURY serves as a model for advancing faculty in their professional careers by providing networking opportunities and support for teaching, research, and service.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemical Research Methods
Gabrielle Black, Charles Lowe, Tarun Anumol, Jessica Bade, Kristin Favela, Yong-Lai Feng, Ann Knolhoff, Andrew Mceachran, Jamie Nunez, Christine Fisher, Kathy Peter, Natalia Soares Quinete, Jon Sobus, Eric Sussman, William Watson, Samanthi Wickramasekara, Antony Williams, Tom Young
Summary: Non-targeted analysis (NTA) using high-resolution mass spectrometry enables the detection and identification of compounds in diverse matrices without prior chemical knowledge. However, there is a need for accessible approaches to map the chemical space in NTA studies. The proposed ChemSpaceTool can help improve method transparency and communication in NTA workflows.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andres Cisneros, Vinicus Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Gotz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet C. Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matias R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, I. I. I. Thomas E. Cheatham, Daniel R. Roe, Adrian Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Jr Kenneth M. Merz
Summary: AmberTools is a free and open-source collection of programs used for setting up, running, and analyzing molecular simulations. This Application note provides a brief description of the newer features found in AmberTools23.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Editorial Material
Chemistry, Analytical
Lewis Botcherby, Ann M. Knolhoff
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)