Article
Endocrinology & Metabolism
Yanwu Yang, Michael D. Glidden, Balamurugan Dhayalan, Alexander N. Zaykov, Yen-Shan Chen, Nalinda P. Wickramasinghe, Richard D. DiMarchi, Michael A. Weiss
Summary: This article investigates the toxic misfolding of diabetes-associated proteins in beta-cells, and proposes a peptide model for classifying related mutations. The study found that the mutant variants exhibit successive structural perturbations, which are correlated with the phenotypic differences in diabetes.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Endocrinology & Metabolism
Balamurugan Dhayalan, Michael D. Glidden, Alexander N. Zaykov, Yen-Shan Chen, Yanwu Yang, Nelson B. Phillips, Faramarz Ismail-Beigi, Mark A. Jarosinski, Richard D. DiMarchi, Michael A. Weiss
Summary: The mutant proinsulin syndrome is a monogenic cause of diabetes mellitus due to toxic misfolding of insulin's biosynthetic precursor. This study used a peptide model to investigate representative clinical mutations and found striking correlations between peptide properties, ER stress, and age of diabetes onset.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Review
Endocrinology & Metabolism
Balamurugan Dhayalan, Deepak Chatterjee, Yen-Shan Chen, Michael A. Weiss
Summary: Analysis of diabetes-associated mutations in the human insulin gene has provided insights into the folding mechanisms of proinsulin, revealing the impact of mutations on pancreatic beta-cell dysfunction and insulin secretion. Studies suggest that conserved residues play a crucial role in folding efficiency and the susceptibility of proinsulin to impaired foldability can contribute to the development of diseases. This highlights the molecular links between biophysical principles and the impact on diseases such as diabetes and obesity.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biology
Quenisha Baldwin, Eleni Panagiotou
Summary: Protein folding, a crucial biological process, involves the relationship between local properties and global properties of proteins. Analysis of protein datasets and single domain proteins suggests that high local topological free energy conformations may impact the folding rates of proteins.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nuno F. B. Oliveira, Filipe E. P. Rodrigues, Joao N. M. Vitorino, Rui J. S. Loureiro, Patricia F. N. Faisca, Miguel Machuqueiro
Summary: The study used the D76N mutant as a model to investigate protein aggregation, finding that hydrophobic interactions play a major role in stabilizing interfaces in a series of dimers at physiological pH. The most stable binding mode exhibits self-limited growth properties, while less stable interfaces can propagate indefinitely to form long polymerized chains.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Yi Kuang, Bin Li, Zilong Wang, Xue Qiao, Min Ye
Summary: Antrodia camphorata is a medicinal mushroom endemic to Taiwan used for the treatment of intoxication, liver injury, cancer, and inflammation. Its terpenoids show various pharmacological activities such as anti-cancer and hepatoprotective effects, making them potentially valuable for medicinal use.
NATURAL PRODUCT REPORTS
(2021)
Review
Chemistry, Medicinal
Anna Pasieka, Eleonora Diamanti, Elisa Uliassi, Maria Laura Bolognesi
Summary: Click chemistry and targeted protein degradation, two flourishing trends in medicinal chemistry. Can they be a winning combination? In this review, we provide the reader with selected examples offered by the combination of these two approaches trying to find a response to this question.
Article
Oncology
Mengling Liu, Xiaojing Xu, Ke Peng, Pengcong Hou, Yitao Yuan, Suyao Li, Xun Sun, Zhongyi Shi, Jiayu Zhang, Yu Dong, Qing Liu, Luoyan Ai, Li Liang, Lu Gan, Qihong Huang, Yiyi Yu, Tianshu Liu
Summary: High expression of heparanase (HPSE) in BRAF V600E-mutant colorectal cancer is associated with poor prognosis. Knockdown of HPSE inhibits tumor proliferation by downregulating Cyclin E2 expression and arresting cell cycle progression. These findings suggest the importance of HPSE in the progression of BRAF V600E-mutant colorectal cancer.
Article
Chemistry, Multidisciplinary
Jan M. Schuemann, J. Philipp Wagner, Andre K. Eckhardt, Henrik Quanz, Peter R. Schreiner
Summary: A comprehensive experimental study was conducted on a molecular balance to measure the effect of different solvents on the equilibrium of folded versus unfolded isomers. The study revealed that London dispersion interactions enthalpically favor the folded state in any measured solvent.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Paola Turina, Piero Fariselli, Emidio Capriotti
Summary: The study of protein folding is crucial for understanding protein function and the relationship between genetics and phenotypes. K-Pro is a new database that collects experimental kinetic data on monomeric proteins with a two-state folding mechanism. It provides a user-friendly interface for browsing and downloading relevant data.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Qin Zhang, Rencai Feng, Renyun Miao, Junbin Lin, Luping Cao, Yanqing Ni, Wensheng Li, Xu Zhao
Summary: Lentinula edodes, a popular edible mushroom in China, is susceptible to high temperatures. However, a mutant strain called Le023M has shown exceptional thermotolerance. Through RNA-seq and qRT-PCR analysis, it was found that heat shock proteins play a crucial role in the thermotolerance of Le023M. Additionally, the accumulation of trehalose, aspartate, and glutamate in Le023M under heat stress contributes to its resistance. These findings provide insights into the thermotolerance mechanisms of Le023M and have potential applications in improving heat stress response and cultivation of L. edodes.
Article
Multidisciplinary Sciences
R. Charlotte Eccleston, David D. Pollock, Richard A. Goldstein
Summary: Epistasis and cooperativity in protein folding are both influenced by networks of energetic interactions within proteins, and their selection can affect each other. Selection for cooperativity may be crucial for predicting protein structure using epistasis measurements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Tae-Eun Kim, Kotaro Tsuboyama, Scott Houliston, Cydney M. Martell, Claire M. Phoumyvong, Alexander Lemak, Hugh K. Haddox, Cheryl H. Arrowsmith, Gabriel J. Rocklin
Summary: Designing new protein structures remains challenging, and our study successfully designed stable aPPa proteins through large-scale design and test cycles, shedding light on the biophysical determinants of folding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Rafayel Petrosyan, Abhishek Narayan, Michael T. Woodside
Summary: Single-molecule force spectroscopy (SMFS) is a powerful tool for studying protein folding dynamics, uncovering energy landscapes of folding, complex folding pathways, mechanisms of chaperones in assisting folding, effects of ribosomes on co-translational folding, and monitoring membrane protein folding.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Irina Sorokina, Arcady R. Mushegian, Eugene V. Koonin
Summary: The prevailing thermodynamic hypothesis of protein folding is called into question due to the lack of strong empirical evidence. Physical theory-based approaches in predicting protein folds have largely failed, except for small proteins. Recent successes in protein structure prediction have been achieved through evolutionary modeling and deep learning methods, but provide no insights into protein folding mechanisms and pathways. An alternative view suggests that most proteins do not occupy the global minimum of free energy, but instead a local minimum on a fluctuating landscape. This view also argues that the majority of proteins require energy-dependent cellular processes for folding, such as interactions with the translation system and chaperones.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Andrew G. P. Maloney, Peter A. Wood, Simon Parsons
Article
Chemistry, Multidisciplinary
Peter A. Wood, Amy A. Sarjeant, Andrey A. Yakovenko, Suzanna C. Ward, Colin R. Groom
CHEMICAL COMMUNICATIONS
(2016)
Article
Chemistry, Multidisciplinary
Andrew G. P. Maloney, Peter A. Wood, Simon Parsons
Article
Chemistry, Multidisciplinary
Peter A. Wood, Clare A. Tovee, Andrew G. P. Maloney, Suzanna C. Ward
CROATICA CHEMICA ACTA
(2018)
Article
Chemistry, Multidisciplinary
Andrew G. P. Maloney, Peter A. Wood, Simon Parsons
Review
Chemistry, Multidisciplinary
Robin Taylor, Peter A. Wood
Article
Chemistry, Multidisciplinary
Matthew G. Reeves, Peter A. Wood, Simon Parsons
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2019)
Article
Chemistry, Multidisciplinary
Albert S. Lundemba, Dikima D. Bibelayi, Peter A. Wood, Juliette Pradon, Zephyrin G. Yav
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2020)
Article
Chemistry, Multidisciplinary
Matthew G. Reeves, Peter A. Wood, Simon Parsons
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2020)
Article
Chemistry, Multidisciplinary
Cameron J. G. Wilson, Tomas Cervenka, Peter A. Wood, Simon Parsons
Summary: We present a Monte Carlo algorithm for calculating the occupied and unoccupied space in crystal structures. This method allows for the detection of discontinuities associated with phase transitions and provides insights into the effects of compression on crystal structures. We applied this method to the study of naphthalene and successfully observed a phase transition previously detected by spectroscopy for the first time using crystallographic data. We also discovered premonitory behavior before phase transitions and crystal collapse at the end of a compression series. The fitted data from 129 high-pressure studies showed that the bulk moduli of networks typically range from 40 to 150 GPa, while those of voids fall within a smaller range of 2-5 GPa. These findings align with the overall narrow range of bulk moduli in molecular solids, approximately 5-20 GPa.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Chemistry, Multidisciplinary
Matthew G. Reeves, Elodie Tailleur, Peter A. Wood, Mathieu Marchivie, Guillaume Chastanet, Philippe Guionneau, Simon Parsons
Summary: Crystal packing energy calculations are used to analyze a family of spin crossover complexes, revealing a linear relationship between transition abruptness and changes in intermolecular interaction energy in the crystal structures. Abrupt transitions are associated with significant stabilising and destabilising changes in intermolecular interaction energies. Different classes of SCO complexes exhibit varying trends in relation to transition abruptness.
Article
Chemistry, Multidisciplinary
Peyman Z. Moghadam, Aurelia Li, Xiao-Wei Liu, Rocio Bueno-Perez, Shu-Dong Wang, Seth B. Wiggin, Peter A. Wood, David Fairen-Jimenez
Article
Chemistry, Multidisciplinary
Nico Giordano, Christine M. Beavers, Konstantin V. Kamenev, William G. Marshall, Stephen A. Moggach, Simon D. Patterson, Simon J. Teat, John E. Warren, Peter A. Wood, Simon Parsons
Article
Chemistry, Physical
Peyman Z. Moghadam, Aurelia Li, Seth B. Wiggin, Andi Tao, Andrew G. P. Maloney, Peter A. Wood, Suzanna C. Ward, David Fairen-Jimenez
CHEMISTRY OF MATERIALS
(2017)
Article
Chemistry, Multidisciplinary
Peter A. Wood, Amy A. Sarjeant, Ian J. Bruno, Clare F. Macrae, Helen E. Maynard-Casely, Matthew Towler