Article
Microbiology
Sunyia Hussain, Janine H. Peterson, Harris D. Bernstein
Summary: The assembly of trimeric porins involves a stepwise process that requires the presence of the Bam complex and LPS. The interaction with LPS is not only essential for trimerization but also for the productive insertion of individual subunits into the lipid bilayer.
Review
Microbiology
Matthew Thomas Doyle, Harris D. Bernstein
Summary: The Omp85 protein superfamily is a group of proteins found in the outer membrane of gram-negative bacteria and bacterial-origin eukaryotic organelles. These proteins are involved in both membrane insertion and translocation of proteins across the outer membrane. Recent studies have uncovered new insights into the functions of these proteins, particularly the well-studied member BamA, which is essential for bacterial barrel assembly and has potential implications for antibiotic development.
ANNUAL REVIEW OF MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ashton N. Combs, Thomas J. Silhavy
Summary: This study reveals a novel role for the periplasmic chaperone Skp in the folding of outer membrane proteins (OMPs) in gram-negative bacteria. Skp removes membrane-integration-defective OMP substrates from the beta-barrel assembly machine (Bam) complex, allowing for clearance of stalled Bam-OMP complexes. Furthermore, Skp acts as an adaptor protein to facilitate the degradation of defective OMP substrates by the periplasmic protease DegP. These findings highlight the importance of Skp in ensuring efficient beta-barrel folding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Karl Lundquist, Evan Billings, Maxine Bi, James Wellnitz, Nicholas Noinaj
Summary: Gram-negative bacteria, mitochondria, and chloroplasts all have outer membranes populated with a type of beta-barrel outer-membrane protein. These proteins play crucial roles in maintaining the viability of their hosts, and recent studies have made significant progress in understanding the biogenesis of these proteins. The structural and functional advancements in the beta-barrel assembly machinery and sorting and assembly machinery provide new insights into the budding mechanism of beta OMPs in these organelles.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Simen Hermansen, David Ryoo, Marcella Orwick-Rydmark, Athanasios Saragliadis, James C. Gumbart, Dirk Linke
Summary: The outer membrane of Gram-negative bacteria acts as an additional diffusion barrier for solutes and nutrients. Outer membrane proteins (OMPs) with large loops protruding into the extracellular environment have potential applications in biotechnology and therapy. This study quantifies the effects of loop insertions on OMP folding and stability using the small outer membrane protein OmpX as a model system. The results show that the length and hydrophobicity of insertions affect OMP folding, and different constructs can fold both in vitro and in their native environment. These findings will improve the design and efficiency of recombinant OMPs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yindi Chu, Zhe Wang, Sebastian Weigold, Derrick Norrell, Enguo Fan
Summary: Research shows that a single TtOmp85 protein can replace the collective function of the five subunits constituting the E. coli BAM, providing new insights into the search for the primitive form of a functional BAM.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Pankaj B. Tiwari, Radhakrishnan Mahalakshmi
Summary: The study reveals that BamA is a substrate-independent promiscuous molecular chaperone, assisting unfolded OMP to overcome the kinetic barrier in assembly and accelerate folding. The primary sequence of OMP remains a vital determining factor in its assembly rate.
Article
Multidisciplinary Sciences
Eve E. Weatherill, Monifa A. Fahie, David P. Marshall, Rachel A. Andvig, Matthew R. Cheetham, Min Chen, Mark Wallace
Summary: Compared to globular proteins, the folding and insertion of beta-barrel membrane proteins are slow but rapid, occurring within seconds upon arrival at the membrane interface. This combination of infrequent yet fast folding events resolves the apparent contradiction between slow ensemble kinetics and typical biomolecular folding timescales.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Sascha Herwig, Joerg H. Kleinschmidt
Summary: Transmembrane proteins play essential roles in all living cells, but the folding and insertion mechanisms of these proteins into membranes are not well understood. In this study, the folding and insertion process of BamA protein into lipid bilayers was investigated, and the formation of beta(9) strand was examined. The results showed that the beta(9) strand forms in a membrane-adsorbed folding intermediate of BamA. This study provides valuable insights into the local secondary structure formation of transmembrane proteins.
Article
Biochemistry & Molecular Biology
Zijian Zhang, David Ryoo, Curtis Balusek, Atanu Acharya, Marcella Orwick Rydmark, Dirk Linke, James C. Gumbart
Summary: The research focused on the transmembrane region of outer-membrane proteins in Gram-negative bacteria, specifically looking at the relationship between beta-barrel size and shape. The study found that smaller beta-barrels maintained a circular shape, while larger variants developed a flattened cross section due to the presence of inward-facing glycines. It was also observed that as the number of beta-strands increased, the fraction of glycines in beta-barrels decreased, possibly indicating an evolutionary role in OMP sequences.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Multidisciplinary Sciences
Neharika Chamachi, Andreas Hartmann, Mai Quynh Ma, Anna Svirina, Georg Krainer, Michael Schlierf
Summary: This study investigates the essential role of periplasmic chaperones, 17-kilodalton protein (Skp) and survival factor A (SurA), in outer membrane protein (OMP) biogenesis. The researchers use single-molecule fluorescence spectroscopy to analyze the conformational dynamics and thermodynamics of Skp and SurA binding to unfolded OmpX and study their disaggre-gase activities. The findings provide insights into the multifaceted functionalities of Skp and SurA and shed light on the balance between conformational flexibility and underlying ener-getics in aiding chaperone action during OMP biogenesis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Taylor Devlin, Dagan C. Marx, Michaela A. Roskopf, Quenton R. Bubb, Ashlee M. Plummer, Karen G. Fleming
Summary: The biogenesis of outer membrane proteins (OMP) in gram-negative bacteria is regulated by a network of periplasmic chaperones, including SurA, Skp, and FkpA. FkpA acts as a chaperone and influences the folding trajectory of OMPs by increasing the folded yield but decreasing the folding rate. It binds to OMPs with an intermediate affinity and has an extensive binding interface.
Article
Multidisciplinary Sciences
Daniel Montezano, Rebecca Bernstein, Matthew M. Copeland, Joanna S. G. Slusky
Summary: By utilizing coevolution data, we have created a large and high-quality database of transmembrane proteins. Our method, IsItABarrel, achieves a balanced accuracy of 95.88% in discriminating among protein classes. Compared to previous algorithms, IsItABarrel shows a high rate of false positives. The database contains a significantly larger number of bacterial TMBB proteins compared to previous sets, and we anticipate it will serve as a valuable resource for researchers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Dung T. Huynh, Wouter S. P. Jong, Gregory M. Koningstein, Peter van Ulsen, Joen Luirink
Summary: Ct-MOMP, a promising subunit-based vaccine candidate, is difficult to express in its native structure in E. coli outer membrane. Co-expression of the Bam complex improved the expression and localization of recombinant Ct-MOMP, leading to correct folding and assembly into a beta-barrel conformation at the cell surface.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Medicinal
Motohiro Fujiu, Katsuki Yokoo, Jun Sato, Satoru Shibuya, Kazuo Komano, Hiroki Kusano, Soichiro Sato, Toshiaki Aoki, Naoki Kohira, Sachi Kanazawa, Ryosuke Watari, Tomoyuki Kawachi, Yuya Hirakawa, Daiki Nagamatsu, Emi Kashiwagi, Hideki Maki, Kenji Yamawaki
Summary: The discovery of an orally absorbed novel antibiotic with good antibacterial activity against resistant strains may be a promising option for treating bacterial infections.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Emily J. Danoff, Karen G. Fleming
Article
Biophysics
Patrick J. Fleming, Karen G. Fleming
BIOPHYSICAL JOURNAL
(2018)
Article
Chemistry, Physical
Henry J. Lessen, Patrick J. Fleming, Karen G. Fleming, Alexander J. Sodt
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2018)
Editorial Material
Physiology
Karen G. Fleming
JOURNAL OF GENERAL PHYSIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Aaron P. Chum, Sophie R. Shoemaker, Patrick J. Fleming, Karen G. Fleming
Article
Chemistry, Multidisciplinary
Henry J. Lessen, Ananya Majumdar, Karen G. Fleming
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Chemistry, Multidisciplinary
Evan S. O'Brien, Brian Fuglestad, Henry J. Lessen, Matthew A. Stetz, Danny W. Lin, Bryan S. Marques, Kushol Gupta, Karen G. Fleming, A. Joshua Wand
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Biophysics
Rebecca F. Alford, Patrick J. Fleming, Karen G. Fleming, Jeffrey J. Gray
BIOPHYSICAL JOURNAL
(2020)
Article
Biochemistry & Molecular Biology
Dagan C. Marx, Mathis J. Leblanc, Ashlee M. Plummer, Susan Krueger, Karen G. Fleming
Article
Multidisciplinary Sciences
Dagan C. Marx, Ashlee M. Plummer, Anneliese M. Faustino, Taylor Devlin, Michaela A. Roskopf, Mathis J. Leblanc, Henry J. Lessen, Barbara T. Amann, Patrick J. Fleming, Susan Krueger, Stephen D. Fried, Karen G. Fleming
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Chemistry, Multidisciplinary
Dagan C. Marx, Karen G. Fleming
Summary: This study determined an empirical correlation between the surface area of nonpolar side chains, transfer free energies, and local water concentration in the membrane, allowing for accurate estimation of Delta G(sc)(0) at any location in the bilayer. Additionally, the calculated interface-to-bilayer transfer free energy values were found to be similar to biological translocon-based transfer free energies, suggesting that the translocon mimics the bilayer interface energetically.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Anastassia A. Vorobieva, Paul White, Binyong Liang, Jim E. Horne, Asim K. Bera, Cameron M. Chow, Stacey Gerben, Sinduja Marx, Alex Kang, Alyssa Q. Stiving, Sophie R. Harvey, Dagan C. Marx, G. Nasir Khan, Karen G. Fleming, Vicki H. Wysocki, David J. Brockwell, Lukas K. Tamm, Sheena E. Radford, David Baker
Summary: Through computational design, researchers successfully developed novel TMBs with no homology to known TMBs, which can reversibly insert and fold into synthetic lipid membranes, and exhibit experimental structures highly similar to computational models. This advancement is expected to facilitate the custom design of pores for various applications.
Article
Biochemistry & Molecular Biology
Dagan C. Marx, Karen G. Fleming
Summary: Membrane protein folding studies have historically been challenging, but recent adaptations of methods have led to success in studying transmembrane proteins. Avoiding aggregation is crucial for the success of these experiments, and they have provided insights into folding trajectories, stabilizing forces, and more defined endpoints.Increased understanding of membrane protein folding in the cell has shown that emerging biophysical principles are largely recapitulated even in complex biological environments.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Biophysics
Patrick J. J. Fleming, John J. J. Correia, Karen G. G. Fleming
Summary: Hydration of biological macromolecules is crucial for their stability and function. Traditional approaches to describe macromolecular hydration using a single parameter have limitations. This study presents a method to calculate two types of hydration: surface shell water and entrained water, which helps explain the hydration problem in hydrodynamics. The combination of these two types of hydration allows accurate calculation of hydrodynamic volume and various macromolecular properties.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2023)
Article
Multidisciplinary Sciences
Philip To, Yingzi Xia, Sea On Lee, Taylor Devlin, Karen G. Fleming, Stephen D. Fried
Summary: The process of protein folding is complex and important, involving cellular factors and processes. Researchers have developed a new method to monitor the structural changes of Escherichia coli proteins in the cell cytosol and with chaperones. The results show that GroEL can assist in refolding the majority of proteins, while DnaK and GroEL have a similar set of proteins that they refold. Additionally, some proteins are not able to be refolded with any chaperones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)