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Vuksanovic N, Clasman JR, Imperiali B, Allen KN. Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA. Protein Sci 2024; 33:e4848. [PMID: 38019455 PMCID: PMC10731488 DOI: 10.1002/pro.4848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
In selected Campylobacter species, the biosynthesis of N-linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane-associated GT-B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N-acetylgalatosamine (GalNAc) from uridine 5'-diphospho-N-acetylgalactosamine (UDP-GalNAc) to undecaprenyl-diphospho-N,N'-diacetylbacillosamine (UndPP-diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane-embedded acceptor and the structural analysis of the complex together with bioinformatics and site-directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″-OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate-specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.
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Affiliation(s)
| | | | - Barbara Imperiali
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
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2
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Lubrano C, Matrone GM, Iaconis G, Santoro F. New Frontiers for Selective Biosensing with Biomembrane-Based Organic Transistors. ACS NANO 2020; 14:12271-12280. [PMID: 33052643 PMCID: PMC8015208 DOI: 10.1021/acsnano.0c07053] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Biosensing plays vital roles in multiple fields, including healthcare monitoring, drug screening, disease diagnosis, and environmental pollution control. In recent years, transistor-based devices have been considered to be valid platforms for fast, low-cost sensing of diverse analytes. Without additional functionalization, however, these devices lack selectivity; several strategies have been developed for the direct immobilization of bioreceptors on the transistor surface to improve detection capabilities. In this scenario, organic transistors have gained attention for their abilities to be coupled to biological systems and to detect biomolecules. In this Perspective, we discuss recent developments in organic-transistor-based biosensors, highlighting how their coupling with artificial membranes provides a strategy to improve sensitivity and selectivity in biosensing applications. Looking at future applications, this class of biosensors represents a breakthrough starting point for implementing multimodal high-throughput screening platforms.
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Affiliation(s)
- Claudia Lubrano
- Tissue
Electronics, Istituto Italiano di Tecnologia, 80125 Naples, Italy
- Dipartimento
di Chimica, Materiali e Produzione Industriale, Università di Napoli Federico II, 80126 Naples, Italy
| | | | - Gennaro Iaconis
- Department
of Medicine, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Francesca Santoro
- Tissue
Electronics, Istituto Italiano di Tecnologia, 80125 Naples, Italy
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3
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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4
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Allen KN, Entova S, Ray LC, Imperiali B. Monotopic Membrane Proteins Join the Fold. Trends Biochem Sci 2019; 44:7-20. [PMID: 30337134 PMCID: PMC6309722 DOI: 10.1016/j.tibs.2018.09.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022]
Abstract
Monotopic membrane proteins, classified by topology, are proteins that embed into a single face of the membrane. These proteins are generally underrepresented in the Protein Data Bank (PDB), but the past decade of research has revealed new examples that allow the description of generalizable features. This Opinion article summarizes shared characteristics including oligomerization states, modes of membrane association, mechanisms of interaction with hydrophobic or amphiphilic substrates, and homology to soluble folds. We also discuss how associations of monotopic enzymes in pathways can be used to promote substrate specificity and product composition. These examples highlight the challenges in structure determination specific to this class of proteins, but also the promise of new understanding from future study of these proteins that reside at the interface.
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Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA; Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Sonya Entova
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leah C Ray
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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5
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Richards MJ, Hsia CY, Singh RR, Haider H, Kumpf J, Kawate T, Daniel S. Membrane Protein Mobility and Orientation Preserved in Supported Bilayers Created Directly from Cell Plasma Membrane Blebs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2963-74. [PMID: 26812542 DOI: 10.1021/acs.langmuir.5b03415] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Membrane protein interactions with lipids are crucial for their native biological behavior, yet traditional characterization methods are often carried out on purified protein in the absence of lipids. We present a simple method to transfer membrane proteins expressed in mammalian cells to an assay-friendly, cushioned, supported lipid bilayer platform using cell blebs as an intermediate. Cell blebs, expressing either GPI-linked yellow fluorescent proteins or neon-green fused transmembrane P2X2 receptors, were induced to rupture on glass surfaces using PEGylated lipid vesicles, which resulted in planar supported membranes with over 50% mobility for multipass transmembrane proteins and over 90% for GPI-linked proteins. Fluorescent proteins were tracked, and their diffusion in supported bilayers characterized, using single molecule tracking and moment scaling spectrum (MSS) analysis. Diffusion was characterized for individual proteins as either free or confined, revealing details of the local lipid membrane heterogeneity surrounding the protein. A particularly useful result of our bilayer formation process is the protein orientation in the supported planar bilayer. For both the GPI-linked and transmembrane proteins used here, an enzymatic assay revealed that protein orientation in the planar bilayer results in the extracellular domains facing toward the bulk, and that the dominant mode of bleb rupture is via the "parachute" mechanism. Mobility, orientation, and preservation of the native lipid environment of the proteins using cell blebs offers advantages over proteoliposome reconstitution or disrupted cell membrane preparations, which necessarily result in significant scrambling of protein orientation and typically immobilized membrane proteins in SLBs. The bleb-based bilayer platform presented here is an important step toward integrating membrane proteomic studies on chip, especially for future studies aimed at understanding fundamental effects of lipid interactions on protein activity and the roles of membrane proteins in disease pathways.
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Affiliation(s)
- Mark J Richards
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Chih-Yun Hsia
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Rohit R Singh
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Huma Haider
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Julia Kumpf
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Toshimitsu Kawate
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Susan Daniel
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
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Nam HJ, Kim I, Bowie JU, Kim S. Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network. Sci Rep 2015; 5:9576. [PMID: 25923201 PMCID: PMC4894438 DOI: 10.1038/srep09576] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/09/2015] [Indexed: 12/15/2022] Open
Abstract
A central question in animal evolution is how multicellular animals evolved from unicellular ancestors. We hypothesize that membrane proteins must be key players in the development of multicellularity because they are well positioned to form the cell-cell contacts and to provide the intercellular communication required for the creation of complex organisms. Here we find that a major mechanism for the necessary increase in membrane protein complexity in the transition from non-metazoan to metazoan life was the new incorporation of domains from soluble proteins. The membrane proteins that have incorporated soluble domains in metazoans are enriched in many of the functions unique to multicellular organisms such as cell-cell adhesion, signaling, immune defense and developmental processes. They also show enhanced protein-protein interaction (PPI) network complexity and centrality, suggesting an important role in the cellular diversification found in complex organisms. Our results expose an evolutionary mechanism that contributed to the development of higher life forms.
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Affiliation(s)
- Hyun-Jun Nam
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Inhae Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095-1570, United States
| | - Sanguk Kim
- 1] School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 790-784, Korea [2] Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
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7
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Yang Z, Wang C, Zhou Q, An J, Hildebrandt E, Aleksandrov LA, Kappes JC, DeLucas LJ, Riordan JR, Urbatsch IL, Hunt JF, Brouillette CG. Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains. Protein Sci 2014; 23:769-89. [PMID: 24652590 PMCID: PMC4093953 DOI: 10.1002/pro.2460] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 03/07/2014] [Accepted: 03/17/2014] [Indexed: 11/06/2022]
Abstract
Detergent interaction with extramembranous soluble domains (ESDs) is not commonly considered an important determinant of integral membrane protein (IMP) behavior during purification and crystallization, even though ESDs contribute to the stability of many IMPs. Here we demonstrate that some generally nondenaturing detergents critically destabilize a model ESD, the first nucleotide-binding domain (NBD1) from the human cystic fibrosis transmembrane conductance regulator (CFTR), a model IMP. Notably, the detergents show equivalent trends in their influence on the stability of isolated NBD1 and full-length CFTR. We used differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy to monitor changes in NBD1 stability and secondary structure, respectively, during titration with a series of detergents. Their effective harshness in these assays mirrors that widely accepted for their interaction with IMPs, i.e., anionic > zwitterionic > nonionic. It is noteworthy that including lipids or nonionic detergents is shown to mitigate detergent harshness, as will limiting contact time. We infer three thermodynamic mechanisms from the observed thermal destabilization by monomer or micelle: (i) binding to the unfolded state with no change in the native structure (all detergent classes); (ii) native state binding that alters thermodynamic properties and perhaps conformation (nonionic detergents); and (iii) detergent binding that directly leads to denaturation of the native state (anionic and zwitterionic). These results demonstrate that the accepted model for the harshness of detergents applies to their interaction with an ESD. It is concluded that destabilization of extramembranous soluble domains by specific detergents will influence the stability of some IMPs during purification.
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Affiliation(s)
- Zhengrong Yang
- Department of Chemistry, University of Alabama at BirminghamBirmingham, Alabama
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Chi Wang
- Department of Biological Sciences, Columbia UniversityNew York, New York
| | - Qingxian Zhou
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Jianli An
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Ellen Hildebrandt
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, Texas
| | - Luba A Aleksandrov
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel HillChapel Hill, North Carolina
- Cystic Fibrosis Treatment and Research Center, The University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - John C Kappes
- Department of Medicine, University of Alabama at BirminghamBirmingham, Alabama
- Birmingham Veterans Affairs Medical Center, Research ServiceBirmingham, Alabama
| | - Lawrence J DeLucas
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
- Department of Optometry, University of Alabama at BirminghamBirmingham, Alabama
| | - John R Riordan
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel HillChapel Hill, North Carolina
- Cystic Fibrosis Treatment and Research Center, The University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, Texas
- Center for Membrane Protein Research, Texas Tech University Health Sciences CenterLubbock, TX
| | - John F Hunt
- Department of Biological Sciences, Columbia UniversityNew York, New York
| | - Christie G Brouillette
- Department of Chemistry, University of Alabama at BirminghamBirmingham, Alabama
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
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8
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Roman EA, González Flecha FL. Kinetics and thermodynamics of membrane protein folding. Biomolecules 2014; 4:354-73. [PMID: 24970219 PMCID: PMC4030980 DOI: 10.3390/biom4010354] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/19/2014] [Accepted: 02/23/2014] [Indexed: 02/06/2023] Open
Abstract
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.
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Affiliation(s)
- Ernesto A Roman
- Laboratory of Molecular Biophysics, Institute of Biochemistry and Biophysical Chemistry, University of Buenos Aires-CONICET, Buenos Aires 1113, Argentina.
| | - F Luis González Flecha
- Laboratory of Molecular Biophysics, Institute of Biochemistry and Biophysical Chemistry, University of Buenos Aires-CONICET, Buenos Aires 1113, Argentina.
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