Article
Chemistry, Physical
Maziar Heidari, Duane Moes, Otto Schullian, Barbara Scalvini, Alireza Mashaghi
Summary: This article introduces a circuit topology-based formalism to define the topology of a complex, which is applied to model polymer chains and protein assemblies. The circuit topology categorizes different forms of chain assemblies. This method is important for analyzing and predicting the mechanistic and evolutionary principles in the design of macromolecular assemblies.
Article
Multidisciplinary Sciences
Ezequiel A. Galpern, Jacopo Marchi, Thierry Mora, Aleksandra M. Walczak, Diego U. Ferreiro
Summary: Repeat proteins, made up of tandem copies of similar amino acid stretches, have diverse folding mechanisms that can be predicted from sequence scores.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Joseph L. Harman, Patrick N. Reardon, Shawn M. Costello, Gus D. Warren, Sophia R. Phillips, Patrick J. Connor, Susan Marqusee, Michael J. Harms
Summary: This study identified a mutation in S100A9 protein that simultaneously increased its stability and disrupted its natural ability to regulate Toll-like receptor 4. Structural analysis revealed that the mutation distorted the hydrophobic binding surface of the protein, leading to its functional impairment. Bioinformatic analysis further showed that Phe residues at both positions 37 and 63 are rarely found in S100A9 proteins from different organisms, suggesting that avoiding pathological stabilizing interactions constrains the evolution of S100A9.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Physics, Multidisciplinary
Giulia Magi Meconi, Ivan R. Sasselli, Valentino Bianco, Jose N. Onuchic, Ivan Coluzza
Summary: Proteins are the indispensable force of life, serving as the structural foundation of living systems and the most efficient molecular machines. Their enzymatic activity surpasses any artificial system in terms of versatility. The remarkable feature of proteins lies in their modular nature, with a diverse range of functions encoded by a simple alphabet of approximately 20 amino acids. The protein folding problem involves encoding all the necessary information within a sequence of these 20 letters. This review explores the progress made in the past 30 years, providing an overview of the state of the art and highlighting applications relevant to the fundamental issues of protein evolution.
REPORTS ON PROGRESS IN PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Jose Alberto Leon-Gonzalez, Perline Flatet, Maria Soledad Juarez-Ramirez, Jose Arcadio Farias-Rico
Summary: This article discusses the role of ribosome in the evolution of protein structures and provides computational and experimental data in support. The study found that folding of proteins can be observed during cotranslational folding in translation process and provides experimental evidence on how proteins may have evolved.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Roberto Del Amparo, Luis Daniel Gonzalez-Vazquez, Laura Rodriguez-Moure, Ugo Bastolla, Miguel Arenas
Summary: Genetic recombination is a common evolutionary mechanism that contributes to molecular diversity. However, its impact on protein folding stability has been less studied compared to point mutations. This study found that although recombination can affect multiple protein sites, it does not significantly increase the elimination of proteins due to insufficient stability compared to mutation events. Recombination disrupts epistatic interactions but does not reduce the overall stability of recombinant proteins. Instead, it amplifies the difference in stability between recombined proteins, leading to phenotypic diversity.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Aleksandra Chikunova, Max P. Manley, Misbha Ud Din Ahmad, Tugce Bilman, Anastassis Perrakis, Marcellus Ubbink
Summary: In class A β-lactamases, the conservation of two residues (Glu37 and Trp229) plays a crucial role in the folding process rather than in the structural and catalytic aspects of the enzyme. These conserved residues are essential for protein resistance and folding.
Review
Microbiology
Jose Arcadio Farias-Rico, Carlos Michel Mourra-Diaz
Summary: Proteins have been crucial throughout the evolution of all organisms, and the origin of life from prebiotic chemistry is still a fascinating question. It is widely accepted that amino acids were available on early Earth, allowing for the formation of peptides. Peptides likely coevolved with ancestral forms of RNA, leading to the development of the ribosome, a complex nanomachine involved in protein synthesis.
Review
Biochemistry & Molecular Biology
Mihaly Badonyi, Joseph A. Marsh
Summary: Recent discoveries have shown that cotranslational assembly is prevalent in proteomes, with various mechanisms enabling the assembly of protein complex subunits on the ribosome. It remains unclear how these complexes have evolved over an extended timescale. This review reflects on historical experiments, breakthroughs in proteome-wide detection of cotranslational assembly, and the remaining technical challenges.
Article
Chemistry, Multidisciplinary
Leonardo Bo, Edoardo Milanetti, Cheng Giuseppe Chen, Giancarlo Ruocco, Andrea Amadei, Marco D'Abramo
Summary: The folding-unfolding thermodynamics of two mutants of Trp-cage miniprotein were characterized using extended molecular dynamics simulations and an advanced statistical-mechanical-based approach. The computational data accurately reproduced the experimental results for the thermophilic mutant, but the mesophilic mutant's thermodynamic behavior could not be reconstructed.
Article
Multidisciplinary Sciences
Rohit Jain, Khaja Muneeruddin, Jeremy Anderson, Michael J. Harms, Scott A. Shaffer, C. Robert Matthews
Summary: The study revealed the folding mechanisms of bacterial IGPS TIM barrel enzyme using HDX-MS, identifying protected sites and stable cores, and emphasizing the key role of hydrophobicity in stabilizing high-energy folding intermediates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
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
Ecology
Tess E. Brewer, Andreas Wagner
Summary: Fast-growing bacteria encode fewer di-prolyl motifs compared to slow-growing ones, especially in highly expressed proteins. Many di-prolyl motifs are found in thermophiles and bacteria with complex, multicellular lifecycles.
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
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
Biotechnology & Applied Microbiology
F. H. Sant'Anna, A. V. Lebedinsky, T. G. Sokolova, F. T. Robb, J. M. Gonzalez
Article
Biochemistry & Molecular Biology
Wirojne Kanoksilapatham, Porranee Keawram, Juan M. Gonzalez, Frank T. Robb
Editorial Material
Microbiology
Jameson D. Voss, Juan C. Leon, Nikhil V. Dhurandhar, Frank T. Robb
FRONTIERS IN MICROBIOLOGY
(2015)
Article
Microbiology
Young Jun An, Sara E. Rowland, Frank T. Robb, Sun-Shin Cha
JOURNAL OF MICROBIOLOGY
(2016)
Article
Microbiology
Phillip J. Brumm, Krishne Gowda, Frank T. Robb, David A. Mead
FRONTIERS IN MICROBIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Garabed Antranikian, Marcel Suleiman, Christian Schaefers, Michael W. W. Adams, Simonetta Bartolucci, Jenny M. Blamey, Nils-Kare Birkeland, Elizaveta Bonch-Osmolovskaya, Milton S. da Costa, Don Cowan, Michael Danson, Patrick Forterre, Robert Kelly, Yoshizumi Ishino, Jennifer Littlechild, Marco Moracci, Kenneth Noll, Tairo Oshima, Frank Robb, Mose Rossi, Helena Santos, Peter Schoenheit, Reinhard Sterner, Rudolf Thauer, Michael Thomm, Juergen Wiegel, Karl Otto Stetter
Article
Multidisciplinary Sciences
Young Jun An, Sara E. Rowland, Jung-Hyun Na, Dario Spigolon, Seung Kon Hong, Yeo Joon Yoon, Jung-Hyun Lee, Frank T. Robb, Sun-Shin Cha
NATURE COMMUNICATIONS
(2017)
Article
Multidisciplinary Sciences
Wonki Min, Francesca Angileri, Haibin Luo, Antonino Lauria, Maruda Shanmugasundaram, Anna Maria Almerico, Francesco Cappello, Everly Conway de Macario, Igor K. Lednev, Alberto J. L. Macario, Frank T. Robb
SCIENTIFIC REPORTS
(2014)
Review
Biology
Everly Conway de Macario, Masafumi Yohda, Alberto J. L. Macario, Frank T. Robb
COMMUNICATIONS BIOLOGY
(2019)
Review
Biochemistry & Molecular Biology
Everly Conway de Macario, Frank T. Robb, Alberto J. L. Macario
FRONTIERS IN MOLECULAR BIOSCIENCES
(2017)
Article
Microbiology
Srijak Bhatnagar, Jonathan H. Badger, Ramana Madupu, Hoda M. Khouri, Elizabeth M. O'Connor, Frank T. Robb, Naomi L. Ward, Jonathan A. Eisen
GENOME ANNOUNCEMENTS
(2015)
Article
Microbiology
Srijak Bhatnagar, Jonathan H. Badger, Ramana Madupu, Hoda M. Khouri, Elizabeth M. O'Connor, Frank T. Robb, Naomi L. Ward, Jonathan A. Eisen
GENOME ANNOUNCEMENTS
(2015)
Article
Microbiology
Alexandra Alexiev, David A. Coil, Jonathan H. Badger, Julie Enticknap, Naomi Ward, Frank T. Robb, Jonathan A. Eisen
GENOME ANNOUNCEMENTS
(2014)
Article
Microbiology
David A. Coil, Jonathan H. Badger, Heather C. Forberger, Florenta Riggs, Ramana Madupu, Nadia Fedorova, Naomi Ward, Frank T. Robb, Jonathan A. Eisen
GENOME ANNOUNCEMENTS
(2014)
Article
Microbiology
David A. Coil, Jonathon R. Lo, Roger Chen, Naomi Ward, Frank T. Robb, Jonathan A. Eisen
GENOME ANNOUNCEMENTS
(2013)