Article
Biochemistry & Molecular Biology
Bryan VanSchouwen, Stephen Boulton, Giuseppe Melacini
Summary: This study using NMR reveals that the contributions of the two substituents of cGMP to the binding affinity of PKG are surprisingly nonadditive, primarily due to mutual protein-ligand conformational selection. The 6-oxo substituent controls the conformational equilibrium of the bound protein, while the 2-NH2 substituent primarily controls the conformational equilibrium of the unbound ligand. Understanding the conformational dynamics of both the protein and ligand is essential to explain the cGMP-versus-cAMP selectivity of PKG.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Eunjeong Lee, Matthew J. Mcleod, Jasmina S. Redzic, Barbara Marcolin, Robert E. Thorne, Pratul Agarwal, Elan Zohar Eisenmesser
Summary: Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that undergoes structural and dynamics changes during its catalytic cycle. Through X-ray crystallography, the apo BLVRB structure was determined for the first time, revealing global changes compared to the holo structure. Amide and Ca chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, while NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Alexa L. Knight, Vinnie Widjaja, George P. Lisi
Summary: Mesophilic and thermophilic enzyme counterparts are studied to understand their functions under harsh conditions. Thermophiles regulate their structural ensemble through intra-protein communication and altered interactions with ligands to function well outside of standard temperature ranges. Recent studies have shown that the enhancement or diminution of allosteric crosstalk can be temperature-dependent and distinguish thermophilic enzymes from their mesophilic counterparts. However, the impact of temperature on allosteric function is understudied compared to other factors such as pH, mutations, or ligands.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Multidisciplinary Sciences
Duncan W. S. MacKenzie, Anna Schaefer, Julia Steckner, Christopher A. Leo, Dalia Naser, Efrosini Artikis, Aron Broom, Travis Ko, Purnank Shah, Mikaela Q. Ney, Elisa Tran, Martin T. J. Smith, Brian Fuglestad, A. Joshua Wand, Charles L. Brooks, Elizabeth M. Meiering
Summary: Allostery is a fundamental process in protein regulation, but understanding the molecular mechanisms behind it is challenging. This study investigates the pH-dependent myristoyl switching in monomeric hisactophilin and reveals the atomistic details and coupling network involved using a combination of experimental measurements and molecular dynamics simulations. The study also demonstrates that small changes in core and surface hydrophobic residues can modulate the energetics of the myristoyl switch.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Jasmina S. Redzic, Michael R. Duff, Ashley Blue, Todd M. Pitts, Pratul Agarwal, Elan Zohar Eisenmesser
Summary: The BLVRB class of enzymes catalyze NADPH-dependent reduction of flavin substrates and play critical roles in cellular redox regulation. Mutations at position T164 can control global micro-millisecond motions and function, and evolutionary changes at distal sites modulate coenzyme binding. Global dynamics within BLVRB consist of partially coupled motions tied to catalytic function.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Federica Maschietto, Erik Zavala, Brandon Allen, J. Patrick Loria, Victor Batista
Summary: In this study, computational modeling and solution NMR spectroscopy were combined to identify an allosteric site in MptpA. The findings suggest that this site plays a crucial role in substrate binding and reaction kinetics.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Drew S. Tack, Peter D. Tonner, Abe Pressman, Nathan D. Olson, Sasha F. Levy, Eugenia F. Romantseva, Nina Alperovich, Olga Vasilyeva, David Ross
Summary: This study quantitatively measured the genotype-phenotype landscape for an allosteric protein, revealing the impact of amino acid substitutions on LacI allostery and systematic sequence-structure-function relationships. It was found that allosteric phenotypes can often be predicted quantitatively with additive or neural-network models, but unpredictable changes may also occur. Additionally, a new band-stop phenotype challenging conventional models of allostery was discovered, arising from combinations of nearly silent amino acid substitutions.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Chemistry, Medicinal
Timothy R. Stachowski, Marcus Fischer
Summary: Protein flexibility is crucial in drug design, especially for targeting dynamic proteins like Hsp90. The analysis of Hsp90 alpha crystal structures revealed different conformations of the lid domain that accommodate chemically distinct ligands. This study highlights the importance of considering protein ensembles and warns against overinterpreting individual crystal structures in drug design.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Michael Jurkutat, Carsten Kattinger, Stefan Tsankov, Richard Reznicek, Andreas Erb, Juergen Haase
Summary: High-temperature superconducting cuprates exhibit a dome-like dependence of their critical temperature (Tc) with doping, but this maximum Tc can be enhanced by applying pressure, a well-known observation for decades. In this study, we used high-pressure anvil cell NMR to investigate this phenomenon and found that pressure increases overall hole doping and leads to a redistribution of holes favoring planar O, similar to the observation of higher maximum Tc for materials with higher hole content at planar O. These results indicate that the pressure-induced enhancement of the maximum Tc points to the same mechanism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Iktae Kim, Alyssa Dubrow, Bryan Zuniga, Baoyu Zhao, Noah Sherer, Abhishek Bastiray, Pingwei Li, Jae-Hyun Cho
Summary: Investigated the influence of strain-specific mutations on the evolution of influenza viruses and found that these mutations play a crucial role in shaping the protein energy landscape and altering the conformational dynamics of tightly packed residues.
NATURE COMMUNICATIONS
(2022)
Article
Automation & Control Systems
Bo-Wei Zhu, Shih-Chih Nian, Ming-Shyan Huang
Summary: This study generated an economic pvT diagram based on sensor data and simulation analysis to predict the quality of injection-molded parts. By combining simulated melting temperature and actual cavity pressure, a pvT curve was constructed and the specific volume of the polymer melt was calculated. Correlation analysis showed that changes in specific volume could predict part size. Additionally, the proposed measurements of the pvT diagram improved the cooling time setting and ensured stable molding quality.
INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Elena Shanina, Sakonwan Kuhaudomlarp, Kanhaya Lal, Peter H. Seeberger, Anne Imberty, Christoph Rademacher
Summary: Carbohydrate-binding proteins, specifically lectins, are promising targets in drug discovery for combating antimicrobial resistance, yet non-carbohydrate drug-like inhibitors are still lacking. A druggable pocket in a beta-propeller lectin from Burkholderia ambifaria has been identified as a potential target for allosteric inhibitors. Future drug-discovery efforts focusing on small molecule inhibitors could benefit from targeting allosteric sites in lectins to combat antibiotic-resistant pathogens.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Lorenz S. Cederbaum, Alexander I. Kuleff
Summary: Interatomic Coulombic decay (ICD) is an efficient electronic decay process that occurs in systems embedded in environments. Quantum light has a significant impact on the ICD process, altering it compared to classical ICD, and allowing for control of ICD rates through manipulation of atomic distribution and orientation. In an electromagnetic cavity, the entanglement of atoms can substantially change ICD rates and be utilized to control the process.
NATURE COMMUNICATIONS
(2021)
Article
Optics
Daigo Oue, Mamoru Matsuo
Summary: In this study, we demonstrate the coupling between the torsional mechanical oscillation of an optical cavity and optical modes by introducing birefringence. We show that the torsional oscillation can be resonantly driven by light.
Article
Chemistry, Physical
Camille Faucon, Pascale Chalier, Christian Sanchez
Summary: Microscopic volume fluctuations in liquids are a reflection of their structure and intermolecular energy, and are associated with cavity formation. This study investigated the relationship between volume fluctuations and cavity formation. Using scaled particle theory calculations, the study provided a relationship between the Gibbs free energy of cavity formation and the average density fluctuations in volume. The correlation between the Gibbs free energy of cavity formation and the isothermal compressibility was confirmed and adjusted using a wide range of liquids.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Trang Van Tran, Hoa Nguyen, Luyen Vu, ChangWoo Lee
Summary: Glutaredoxin 3 (Grx3) is a redox protein that maintains structural integrity and glutathione (GSH) binding capabilities across different temperatures. This study investigates the roles of specific bonds in Grx3's structure and function, and how psychrophilic Grx3 variants adapt to cold environments. The highly conserved Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond are crucial for stabilizing the structure and catalytic activity of Grx3. Psychrophilic variants of Grx3 have adapted to cold environments by reducing GSH binding and increasing structural flexibility.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Amanda Lais de Souza Coto, Arthur Alexandre Pereira, Sabrina Dorta Oliveira, Milene Nobrega de Oliveira Moritz, Arthur Moraes Franco da Rocha, Paulo Roberto Dores-Silva, Noeli Soares Melo da Silva, Ana Rita de Araujo Nogueira, Lisandra Marques Gava, Thiago Vagas Seraphim, Julio Cesar Borges
Summary: J-domain proteins form a large molecular chaperone family involved in proteostasis processes, with hDjC20 playing a vital role in mitochondria and being heavily influenced by the presence of Zn+2.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Meiling Zhang, Jiaxiang Zhang, Yan Liang, Shicheng Tian, Shuyang Xie, Tong Zhou, Qin Wang
Summary: This study determined the crystal structures of RGLG2 VWA domain in Arabidopsis thaliana, revealing that Ca2+ ions act as regulators and affect the conformational change of RGLG2-VWA domain.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Alexandra Bork, Sander H. J. Smits, Lutz Schmitt
Summary: This study reveals the structure and calcium ion binding properties of CBL1 protein, and proposes a binding model of CBL1 for Ca2+. Additionally, it provides preliminary insights into the formation of the dimer interface of CBL1.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Evgeniia V. Leisi, Andrey V. Moiseenko, Sofia S. Kudryavtseva, Denis V. Pozdyshev, Vladimir I. Muronetz, Lidia P. Kurochkina
Summary: The pathogenesis of prion diseases involves the transformation of prion protein into an insoluble form. This study found that two phage chaperonins can promote the fibrillation of prion protein in an ATP-dependent manner, resulting in the formation of less toxic large clusters. These fibrils differ in morphology and properties from those formed spontaneously in acidic pH with denaturants.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Gaurab Chowdhury, Saroj Biswas, Yuthika Dholey, Puja Panja, Sumit Das, Subrata Adak
Summary: Magnesium is an important divalent cation for regulating enzyme activity. The binding of Mg2+ through the PAS domain inhibits phosphoglycerate kinase (PGK) activity in LmPAS-PGK at neutral pH, but PGK activity is derepressed at acidic pH. Mutation studies revealed that the Asp-4 residue is crucial for Mg2+ binding at neutral pH.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Shima Ghaedizadeh, Majid Zeinali, Bahareh Dabirmanesh, Behnam Rasekh, Khosrow Khajeh, Ali Mohammad Banaei-Moghaddam
Summary: Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies can increase the rate of CO2 absorption from industrial flue gases. This study successfully improved the thermostability of a known hyperthermostable carbonic anhydrase through rational engineering of a single-point mutation.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Khaled A. Elnahriry, Dorothy C. C. Wai, Lauren M. Ashwood, Muhammad Umair Naseem, Tibor G. Szanto, Shaodong Guo, Gyorgy Panyi, Peter J. Prentis, Raymond S. Norton
Summary: Sea anemone venom contains a peptide called Tst2, which shows sequence similarity to peptides that interact with various ion channels. Recombinant Tst2 was successfully produced and its structure and function were studied. The results showed that Tst2 is an inhibitor of the TRPV1 channel.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)