1
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Scott BM, Chen SK, Van Nynatten A, Liu J, Schott RK, Heon E, Peisajovich SG, Chang BSW. Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin. J Mol Evol 2024; 92:61-71. [PMID: 38324225 DOI: 10.1007/s00239-024-10154-3] [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: 10/17/2023] [Accepted: 12/22/2023] [Indexed: 02/08/2024]
Abstract
Eukaryotic cells use G protein-coupled receptors (GPCRs) to convert external stimuli into internal signals to elicit cellular responses. However, how mutations in GPCR-coding genes affect GPCR activation and downstream signaling pathways remain poorly understood. Approaches such as deep mutational scanning show promise in investigations of GPCRs, but a high-throughput method to measure rhodopsin activation has yet to be achieved. Here, we scale up a fluorescent reporter assay in budding yeast that we engineered to study rhodopsin's light-activated signal transduction. Using this approach, we measured the mutational effects of over 1200 individual human rhodopsin mutants, generated by low-frequency random mutagenesis of the GPCR rhodopsin (RHO) gene. Analysis of the data in the context of rhodopsin's three-dimensional structure reveals that transmembrane helices are generally less tolerant to mutations compared to flanking helices that face the lipid bilayer, which suggest that mutational tolerance is contingent on both the local environment surrounding specific residues and the specific position of these residues in the protein structure. Comparison of functional scores from our screen to clinically identified rhodopsin disease variants found many pathogenic mutants to be loss of function. Lastly, functional scores from our assay were consistent with a complex counterion mechanism involved in ligand-binding and rhodopsin activation. Our results demonstrate that deep mutational scanning is possible for rhodopsin activation and can be an effective method for revealing properties of mutational tolerance that may be generalizable to other transmembrane proteins.
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Affiliation(s)
- Benjamin M Scott
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Steven K Chen
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Jing Liu
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Department of Biology and Centre for Vision Research, York University, Toronto, ON, Canada
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Elise Heon
- Department of Ophthalmology, Hospital for Sick Children, Toronto, ON, Canada
| | - Sergio G Peisajovich
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.
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2
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. Angew Chem Int Ed Engl 2023; 62:e202305694. [PMID: 37329506 PMCID: PMC7615181 DOI: 10.1002/anie.202305694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/20/2023] [Accepted: 06/15/2023] [Indexed: 06/19/2023]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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3
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202305694. [PMID: 38516403 PMCID: PMC10953453 DOI: 10.1002/ange.202305694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 03/23/2024]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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4
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AL Mughram MH, Catalano C, Herrington NB, Safo MK, Kellogg GE. 3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins. Front Mol Biosci 2023; 10:1116868. [PMID: 37056722 PMCID: PMC10086146 DOI: 10.3389/fmolb.2023.1116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 03/30/2023] Open
Abstract
The aliphatic hydrophobic amino acid residues—alanine, isoleucine, leucine, proline and valine—are among the most common found in proteins. Their structural role in proteins is seemingly obvious: engage in hydrophobic interactions to stabilize secondary, and to a lesser extent, tertiary and quaternary structure. However, favorable hydrophobic interactions involving the sidechains of these residue types are generally less significant than the unfavorable set arising from interactions with polar atoms. Importantly, the constellation of interactions between residue sidechains and their environments can be recorded as three-dimensional maps that, in turn, can be clustered. The clustered average map sets compose a library of interaction profiles encoding interaction strengths, interaction types and the optimal 3D position for the interacting partners. This library is backbone angle-dependent and suggests solvent and lipid accessibility for each unique interaction profile. In this work, in addition to analysis of soluble proteins, a large set of membrane proteins that contained optimized artificial lipids were evaluated by parsing the structures into three distinct components: soluble extramembrane domain, lipid facing transmembrane domain, core transmembrane domain. The aliphatic residues were extracted from each of these sets and passed through our calculation protocol. Notable observations include: the roles of aliphatic residues in soluble proteins and in the membrane protein’s soluble domains are nearly identical, although the latter are slightly more solvent accessible; by comparing maps calculated with sidechain-lipid interactions to maps ignoring those interactions, the potential extent of residue-lipid and residue-interactions can be assessed and likely exploited in structure prediction and modeling; amongst these residue types, the levels of lipid engagement show isoleucine as the most engaged, while the other residues are largely interacting with neighboring helical residues.
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Affiliation(s)
- Mohammed H. AL Mughram
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Noah B. Herrington
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Martin K. Safo
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Glen E. Kellogg
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
- *Correspondence: Glen E. Kellogg,
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5
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Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale. Int J Mol Sci 2022; 23:ijms23073515. [PMID: 35408876 PMCID: PMC8999133 DOI: 10.3390/ijms23073515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
A novel resemblance-ranking peptide library with 160,000 10-meric peptides was designed to search for selective binders to antibodies. The resemblance-ranking principle enabled the selection of sequences that are most similar to the human peptidome. The library was synthesized with ultra-high-density peptide arrays. As proof of principle, screens for selective binders were performed for the therapeutic anti-CD20 antibody rituximab. Several features in the amino acid composition of antibody-binding peptides were identified. The selective affinity of rituximab increased with an increase in the number of hydrophobic amino acids in a peptide, mainly tryptophan and phenylalanine, while a total charge of the peptide remained relatively small. Peptides with a higher affinity exhibited a lower sum helix propensity. For the 30 strongest peptide binders, a substitutional analysis was performed to determine dissociation constants and the invariant amino acids for binding to rituximab. The strongest selective peptides had a dissociation constant in the hundreds of the nano-molar range. The substitutional analysis revealed a specific hydrophobic epitope for rituximab. To show that conformational binders can, in principle, be detected in array format, cyclic peptide substitutions that are similar to the target of rituximab were investigated. Since the specific binders selected via the resemblance-ranking peptide library were based on the hydrophobic interactions that are widespread in the world of biomolecules, the library can be used to screen for potential linear epitopes that may provide information about the cross-reactivity of antibodies.
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6
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Lewis AJO, Hegde RS. A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC. BMC Biol 2021; 19:266. [PMID: 34911545 PMCID: PMC8675477 DOI: 10.1186/s12915-021-01171-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Protein transporters translocate hydrophilic segments of polypeptide across hydrophobic cell membranes. Two protein transporters are ubiquitous and date back to the last universal common ancestor: SecY and YidC. SecY consists of two pseudosymmetric halves, which together form a membrane-spanning protein-conducting channel. YidC is an asymmetric molecule with a protein-conducting hydrophilic groove that partially spans the membrane. Although both transporters mediate insertion of membrane proteins with short translocated domains, only SecY transports secretory proteins and membrane proteins with long translocated domains. The evolutionary origins of these ancient and essential transporters are not known. RESULTS The features conserved by the two halves of SecY indicate that their common ancestor was an antiparallel homodimeric channel. Structural searches with SecY's halves detect exceptional similarity with YidC homologs. The SecY halves and YidC share a fold comprising a three-helix bundle interrupted by a helical hairpin. In YidC, this hairpin is cytoplasmic and facilitates substrate delivery, whereas in SecY, it is transmembrane and forms the substrate-binding lateral gate helices. In both transporters, the three-helix bundle forms a protein-conducting hydrophilic groove delimited by a conserved hydrophobic residue. Based on these similarities, we propose that SecY originated as a YidC homolog which formed a channel by juxtaposing two hydrophilic grooves in an antiparallel homodimer. We find that archaeal YidC and its eukaryotic descendants use this same dimerisation interface to heterodimerise with a conserved partner. YidC's sufficiency for the function of simple cells is suggested by the results of reductive evolution in mitochondria and plastids, which tend to retain SecY only if they require translocation of large hydrophilic domains. CONCLUSIONS SecY and YidC share previously unrecognised similarities in sequence, structure, mechanism, and function. Our delineation of a detailed correspondence between these two essential and ancient transporters enables a deeper mechanistic understanding of how each functions. Furthermore, key differences between them help explain how SecY performs its distinctive function in the recognition and translocation of secretory proteins. The unified theory presented here explains the evolution of these features, and thus reconstructs a key step in the origin of cells.
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Affiliation(s)
- Aaron J O Lewis
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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7
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Lara Ortiz MT, Martinell García V, Del Rio G. Saturation Mutagenesis of the Transmembrane Region of HokC in Escherichia coli Reveals Its High Tolerance to Mutations. Int J Mol Sci 2021; 22:ijms221910359. [PMID: 34638709 PMCID: PMC8509063 DOI: 10.3390/ijms221910359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Cells adapt to different stress conditions, such as the antibiotics presence. This adaptation sometimes is achieved by changing relevant protein positions, of which the mutability is limited by structural constrains. Understanding the basis of these constrains represent an important challenge for both basic science and potential biotechnological applications. To study these constraints, we performed a systematic saturation mutagenesis of the transmembrane region of HokC, a toxin used by Escherichia coli to control its own population, and observed that 92% of single-point mutations are tolerated and that all the non-tolerated mutations have compensatory mutations that reverse their effect. We provide experimental evidence that HokC accumulates multiple compensatory mutations that are found as correlated mutations in the HokC family multiple sequence alignment. In agreement with these observations, transmembrane proteins show higher probability to present correlated mutations and are less densely packed locally than globular proteins; previous mutagenesis results on transmembrane proteins further support our observations on the high tolerability to mutations of transmembrane regions of proteins. Thus, our experimental results reveal the HokC transmembrane region high tolerance to loss-of-function mutations that is associated with low sequence conservation and high rate of correlated mutations in the HokC family sequences alignment, which are features shared with other transmembrane proteins.
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8
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Bevacqua A, Bakshi S, Xia Y. Principal component analysis of alpha-helix deformations in transmembrane proteins. PLoS One 2021; 16:e0257318. [PMID: 34525125 PMCID: PMC8443038 DOI: 10.1371/journal.pone.0257318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
α-helices are deformable secondary structural components regularly observed in protein folds. The overall flexibility of an α-helix can be resolved into constituent physical deformations such as bending in two orthogonal planes and twisting along the principal axis. We used Principal Component Analysis to identify and quantify the contribution of each of these dominant deformation modes in transmembrane α-helices, extramembrane α-helices, and α-helices in soluble proteins. Using three α-helical samples from Protein Data Bank entries spanning these three cellular contexts, we determined that the relative contributions of these modes towards total deformation are independent of the α-helix's surroundings. This conclusion is supported by the observation that the identities of the top three deformation modes, the scaling behaviours of mode eigenvalues as a function of α-helix length, and the percentage contribution of individual modes on total variance were comparable across all three α-helical samples. These findings highlight that α-helical deformations are independent of cellular location and will prove to be valuable in furthering the development of flexible templates in de novo protein design.
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Affiliation(s)
- Alexander Bevacqua
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Sachit Bakshi
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Yu Xia
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
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9
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Principles and Methods in Computational Membrane Protein Design. J Mol Biol 2021; 433:167154. [PMID: 34271008 DOI: 10.1016/j.jmb.2021.167154] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 01/13/2023]
Abstract
After decades of progress in computational protein design, the design of proteins folding and functioning in lipid membranes appears today as the next frontier. Some notable successes in the de novo design of simplified model membrane protein systems have helped articulate fundamental principles of protein folding, architecture and interaction in the hydrophobic lipid environment. These principles are reviewed here, together with the computational methods and approaches that were used to identify them. We provide an overview of the methodological innovations in the generation of new protein structures and functions and in the development of membrane-specific energy functions. We highlight the opportunities offered by new machine learning approaches applied to protein design, and by new experimental characterization techniques applied to membrane proteins. Although membrane protein design is in its infancy, it appears more reachable than previously thought.
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10
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Dhar R, Feehan R, Slusky JSG. Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels. J Phys Chem B 2021; 125:3622-3628. [PMID: 33797916 DOI: 10.1021/acs.jpcb.1c00878] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Up-and-down β-barrel topology exists in both the membrane and soluble environment. By comparing features of these structurally similar proteins, we can determine what features are particular to the environment rather than the fold. Here we compare structures of membrane β-barrels to soluble β-barrels and evaluate their relative size, shape, amino acid composition, hydrophobicity, and periodicity. We find that membrane β-barrels are generally larger than soluble β-barrels, with more strands per barrel and more amino acids per strand, making them wider and taller. We also find that membrane β-barrels are inside-out soluble β-barrels. The inward region of membrane β-barrels has similar hydrophobicity to the outward region of soluble β-barrels, and the outward region of membrane β-barrels has similar hydrophobicity to the inward region of the soluble β-barrels. Moreover, even though both types of β-barrel have been assumed to have strands with amino acids that alternate in direction and hydrophobicity, we find that the membrane β-barrels have more regular alternation than soluble β-barrels. These features give insight into how membrane barrels maintain their fold and function in the membrane.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Ryan Feehan
- Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States
| | - Joanna S G Slusky
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States.,Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States
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11
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Farias AB, Candiotto G, Siragusa L, Goracci L, Cruciani G, Oliveira ERA, Horta BAC. Targeting Nsp9 as an anti-SARS-CoV-2 strategy. NEW J CHEM 2021. [DOI: 10.1039/d0nj04909c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Non-structural protein 9 (Nsp9) plays a key role in viral replication of coronavirus and represents a promising target for anti-SARS-CoV-2 strategies.
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Affiliation(s)
- André B. Farias
- Instituto de Química
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
- Brazil
| | - Graziâni Candiotto
- Instituto de Química
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
- Brazil
| | | | - Laura Goracci
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- Perugia
- Italy
| | - Gabriele Cruciani
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- Perugia
- Italy
| | - Edson R. A. Oliveira
- Department of Microbiology and Immunology
- University of Illinois at Chicago
- Chicago
- USA
| | - Bruno A. C. Horta
- Instituto de Química
- Universidade Federal do Rio de Janeiro
- Rio de Janeiro
- Brazil
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12
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Zaucha J, Heinzinger M, Kulandaisamy A, Kataka E, Salvádor ÓL, Popov P, Rost B, Gromiha MM, Zhorov BS, Frishman D. Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins. Brief Bioinform 2020; 22:5872174. [PMID: 32672331 DOI: 10.1093/bib/bbaa132] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022] Open
Abstract
Membrane proteins are unique in that they interact with lipid bilayers, making them indispensable for transporting molecules and relaying signals between and across cells. Due to the significance of the protein's functions, mutations often have profound effects on the fitness of the host. This is apparent both from experimental studies, which implicated numerous missense variants in diseases, as well as from evolutionary signals that allow elucidating the physicochemical constraints that intermembrane and aqueous environments bring. In this review, we report on the current state of knowledge acquired on missense variants (referred to as to single amino acid variants) affecting membrane proteins as well as the insights that can be extrapolated from data already available. This includes an overview of the annotations for membrane protein variants that have been collated within databases dedicated to the topic, bioinformatics approaches that leverage evolutionary information in order to shed light on previously uncharacterized membrane protein structures or interaction interfaces, tools for predicting the effects of mutations tailored specifically towards the characteristics of membrane proteins as well as two clinically relevant case studies explaining the implications of mutated membrane proteins in cancer and cardiomyopathy.
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Affiliation(s)
- Jan Zaucha
- Department of Bioinformatics of the TUM School of Life Sciences Weihenstephan in Freising, Germany
| | - Michael Heinzinger
- Department of Informatics, Bioinformatics and Computational Biology of the TUM Faculty of Informatics in Garching, Germany
| | - A Kulandaisamy
- Department of Biotechnology of the IIT Bhupat and Jyoti Mehta School of BioSciences in Madras, India
| | - Evans Kataka
- Department of Bioinformatics of the TUM School of Life Sciences Weihenstephan in Freising, Germany
| | - Óscar Llorian Salvádor
- Department of Informatics, Bioinformatics and Computational Biology of the TUM Faculty of Informatics in Garching, Germany
| | - Petr Popov
- Center for Computational and Data-Intensive Science and Engineering of the Skolkovo Institute of Science and Technology in Moscow, Russia
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology at the TUM Faculty of Informatics in Garching, Germany
| | | | - Boris S Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University in Hamilton, Canada
| | - Dmitrij Frishman
- Department of Bioinformatics at the TUM School of Life Sciences Weihenstephan in Freising, Germany
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13
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Westerfield JM, Barrera FN. Membrane receptor activation mechanisms and transmembrane peptide tools to elucidate them. J Biol Chem 2019; 295:1792-1814. [PMID: 31879273 DOI: 10.1074/jbc.rev119.009457] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Single-pass membrane receptors contain extracellular domains that respond to external stimuli and transmit information to intracellular domains through a single transmembrane (TM) α-helix. Because membrane receptors have various roles in homeostasis, signaling malfunctions of these receptors can cause disease. Despite their importance, there is still much to be understood mechanistically about how single-pass receptors are activated. In general, single-pass receptors respond to extracellular stimuli via alterations in their oligomeric state. The details of this process are still the focus of intense study, and several lines of evidence indicate that the TM domain (TMD) of the receptor plays a central role. We discuss three major mechanistic hypotheses for receptor activation: ligand-induced dimerization, ligand-induced rotation, and receptor clustering. Recent observations suggest that receptors can use a combination of these activation mechanisms and that technical limitations can bias interpretation. Short peptides derived from receptor TMDs, which can be identified by screening or rationally developed on the basis of the structure or sequence of their targets, have provided critical insights into receptor function. Here, we explore recent evidence that, depending on the target receptor, TMD peptides cannot only inhibit but also activate target receptors and can accommodate novel, bifunctional designs. Furthermore, we call for more sharing of negative results to inform the TMD peptide field, which is rapidly transforming into a suite of unique tools with the potential for future therapeutics.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996.
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14
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Vicente FM, González-Garcia M, Diaz Pico E, Moreno-Castillo E, Garay HE, Rosi PE, Jimenez AM, Campos-Delgado JA, Rivera DG, Chinea G, Pietro RCL, Stenger S, Spellerberg B, Kubiczek D, Bodenberger N, Dietz S, Rosenau F, Paixão MW, Ständker L, Otero-González AJ. Design of a Helical-Stabilized, Cyclic, and Nontoxic Analogue of the Peptide Cm-p5 with Improved Antifungal Activity. ACS OMEGA 2019; 4:19081-19095. [PMID: 31763531 PMCID: PMC6868880 DOI: 10.1021/acsomega.9b02201] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/04/2019] [Indexed: 05/15/2023]
Abstract
Following the information obtained by a rational design study, a cyclic and helical-stabilized analogue of the peptide Cm-p5 was synthetized. The cyclic monomer showed an increased activity in vitro against Candida albicans and Candida parapsilosis, compared to Cm-p5. Initially, 14 mutants of Cm-p5 were synthesized following a rational design to improve the antifungal activity and pharmacological properties. Antimicrobial testing showed that the activity was lost in each of these 14 analogues, suggesting, as a main conclusion, that a Glu-His salt bridge could stabilize Cm-p5 helical conformation during the interaction with the plasma membrane. A derivative, obtained by substitution of Glu and His for Cys, was synthesized and oxidized with the generation of a cyclic monomer with improved antifungal activity. In addition, two dimers were generated during the oxidation procedure, a parallel and antiparallel one. The dimers showed a helical secondary structure in water, whereas the cyclic monomer only showed this conformation in SDS. Molecular dynamic simulations confirmed the helical stabilizations for all of them, therefore indicating the possible essential role of the Glu-His salt bridge. In addition, the antiparallel dimer showed a moderate activity against Pseudomonas aeruginosa and a significant activity against Listeria monocytogenes. Neither the cyclic monomer nor the dimers were toxic against macrophages or THP-1 human cells. Due to its increased capacity for fungal control compared to fluconazole, its low cytotoxicity, together with a stabilized α-helix and disulfide bridges, that may advance its metabolic stability, and in vivo activity, the new cyclic Cm-p5 monomer represents a potential systemic antifungal therapeutic candidate.
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Affiliation(s)
- Fidel
E. Morales Vicente
- General
Chemistry Department, Faculty of Chemistry and Center for Natural Products Research,
Faculty of Chemistry, University of Havana, Zapata y G, 10400 La Habana, Cuba
- Synthetic
Peptides Group, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, 10600 La Habana, Cuba
- Center
of Excellence for Research in Sustainable Chemistry (CERSusChem),
Department of Chemistry, Federal University
of São Carlos-UFSCar, São Paulo 13565-905, Brazil
| | - Melaine González-Garcia
- Center
for Protein Studies, Faculty of Biology, University of Havana, 25 and I, 10400 La Habana, Cuba
| | - Erbio Diaz Pico
- Synthetic
Peptides Group, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, 10600 La Habana, Cuba
| | - Elena Moreno-Castillo
- General
Chemistry Department, Faculty of Chemistry and Center for Natural Products Research,
Faculty of Chemistry, University of Havana, Zapata y G, 10400 La Habana, Cuba
| | - Hilda E. Garay
- Synthetic
Peptides Group, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, 10600 La Habana, Cuba
| | - Pablo E. Rosi
- Department
of Inorganic Chemistry, Analytical and Physical Chemistry, Facultad
de Ciencias Exactas y Naturales, Universidad
de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Asiel Mena Jimenez
- General
Chemistry Department, Faculty of Chemistry and Center for Natural Products Research,
Faculty of Chemistry, University of Havana, Zapata y G, 10400 La Habana, Cuba
| | - Jose A. Campos-Delgado
- Center
of Excellence for Research in Sustainable Chemistry (CERSusChem),
Department of Chemistry, Federal University
of São Carlos-UFSCar, São Paulo 13565-905, Brazil
| | - Daniel G. Rivera
- General
Chemistry Department, Faculty of Chemistry and Center for Natural Products Research,
Faculty of Chemistry, University of Havana, Zapata y G, 10400 La Habana, Cuba
| | - Glay Chinea
- Synthetic
Peptides Group, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, 10600 La Habana, Cuba
| | - Rosemeire C. L.
R. Pietro
- Laboratory
of Pharmaceutical Biotechnology, Department of Drugs and Medicines,
School of Pharmaceutical Sciences, UNESP, Araraquara 14800-900, Brazil
| | - Steffen Stenger
- Institute
of Medical Microbiology and Hygiene, University
Clinic of Ulm, Robert Koch Str. 8, Ulm D-89081, Germany
| | - Barbara Spellerberg
- Institute
of Medical Microbiology and Hygiene, University
Clinic of Ulm, Robert Koch Str. 8, Ulm D-89081, Germany
| | - Dennis Kubiczek
- Institute
of Pharmaceutical Biotechnology, Ulm University, James-Frank-Ring N27, 89081 Ulm, Germany
| | - Nicholas Bodenberger
- Institute
of Pharmaceutical Biotechnology, Ulm University, James-Frank-Ring N27, 89081 Ulm, Germany
| | - Steffen Dietz
- Institute
of Pharmaceutical Biotechnology, Ulm University, James-Frank-Ring N27, 89081 Ulm, Germany
| | - Frank Rosenau
- Institute
of Pharmaceutical Biotechnology, Ulm University, James-Frank-Ring N27, 89081 Ulm, Germany
| | - Márcio Weber Paixão
- Center
of Excellence for Research in Sustainable Chemistry (CERSusChem),
Department of Chemistry, Federal University
of São Carlos-UFSCar, São Paulo 13565-905, Brazil
- E-mail: (W.P.)
| | - Ludger Ständker
- Core
Facility for Functional Peptidomics, Ulm Peptide Pharmaceuticals (U-PEP),
University Ulm, Faculty of Medicine, Ulm
University, 89081 Ulm, Germany
- E-mail: (L.S.)
| | - Anselmo J. Otero-González
- Center
for Protein Studies, Faculty of Biology, University of Havana, 25 and I, 10400 La Habana, Cuba
- E-mail: (A.J.O.-G.)
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15
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Dimerization of Coronavirus nsp9 with Diverse Modes Enhances Its Nucleic Acid Binding Affinity. J Virol 2018; 92:JVI.00692-18. [PMID: 29925659 DOI: 10.1128/jvi.00692-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/29/2018] [Indexed: 01/07/2023] Open
Abstract
Coronaviruses pose serious health threats to humans and other animals. Understanding the mechanisms of their replication has important implications for global health and economic stability. Nonstructural protein 9 (nsp9) is an essential RNA binding protein for coronavirus replication. However, the mechanisms of the dimerization and nucleic acid binding of nsp9 remain elusive. Here, we report four crystal structures, including wild-type porcine delta coronavirus (PDCoV) nsp9, PDCoV nsp9-ΔN7 (N-terminal 7 amino acids deleted), wild-type porcine epidemic diarrhea virus (PEDV) nsp9, and PEDV nsp9-C59A mutant. These structures reveal the diverse dimerization forms of coronavirus nsp9. We first found that the N-finger of nsp9 from PDCoV plays a critical role in dimerization. Meanwhile, PEDV nsp9 is distinguished by the presence of a disulfide bond in the dimer interface. Interestingly, size exclusion chromatography and analytical ultracentrifugation analyses indicate that the PDCoV nsp9-ΔN7 and PEDV nsp9-C59A mutants are monomeric in solution. In addition, electrophoretic mobility shift assays and microscale thermophoresis analysis indicate that the monomeric forms of PDCoV nsp9 and PEDV nsp9 still have nucleic acid binding affinity, although it is lower than that of the wild type. Our results show that the diverse dimerization forms of coronavirus nsp9 proteins enhance their nucleic acid binding affinity.IMPORTANCE Coronaviruses cause widespread respiratory, gastrointestinal, and central nervous system diseases in humans and other animals, threatening human health and causing economic loss. Coronavirus nsp9, a member of the replication complex, is an important RNA binding subunit in the RNA-synthesizing machinery of all coronaviruses. However, the mechanisms of the dimerization and nucleic acid binding of nsp9 remain elusive. In this study we determined the nsp9 crystal structures of PDCoV and PEDV. We first found that the N-finger of nsp9 from PDCoV plays a critical role in dimerization. Meanwhile, PEDV nsp9 is distinguished by the presence of a disulfide bond in the dimer interface. This study provides a structural and functional basis for understanding the mechanism of dimerization and shows that the diverse dimerization modes of coronavirus nsp9 proteins enhance their nucleic acid binding affinity. Importantly, these findings may provide a new insight for antiviral drug development.
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16
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Yaffe D, Forrest LR, Schuldiner S. The ins and outs of vesicular monoamine transporters. J Gen Physiol 2018; 150:671-682. [PMID: 29666153 PMCID: PMC5940252 DOI: 10.1085/jgp.201711980] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/26/2018] [Indexed: 01/31/2023] Open
Abstract
Yaffe et al. review structure-guided studies that have provided insight into the mechanism of proton-monoamine antiport by VMATs. The H+-coupled vesicular monoamine transporter (VMAT) is a transporter essential for life. VMAT mediates packaging of the monoamines serotonin, dopamine, norepinephrine, and histamine from the neuronal cytoplasm into presynaptic vesicles, which is a key step in the regulated release of neurotransmitters. However, a detailed understanding of the mechanism of VMAT function has been limited by the lack of availability of high-resolution structural data. In recent years, a series of studies guided by homology models has revealed significant insights into VMAT function, identifying residues that contribute to the binding site and to specific steps in the transport cycle. Moreover, to characterize the conformational transitions that occur upon binding of the substrate and coupling ion, we have taken advantage of the unique and powerful pharmacology of VMAT as well as of mutants that affect the conformational equilibrium of the protein and shift it toward defined conformations. This has allowed us to identify an important role for the proton gradient in driving a shift from lumen-facing to cytoplasm-facing conformations.
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Affiliation(s)
- Dana Yaffe
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Shimon Schuldiner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
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17
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Exploring conformational states and helical packings in the P2X receptor transmembrane domain by molecular dynamics simulation. J Biol Phys 2018; 44:331-344. [PMID: 29611030 DOI: 10.1007/s10867-018-9493-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/19/2018] [Indexed: 02/05/2023] Open
Abstract
The P2X receptor is a trimeric transmembrane protein that acts as an ATP-gated ion channel. Its transmembrane domain (TMD) contains only six helices and three of them, the M2 helices, line the ion conduction pathway. Here, using molecular dynamics simulation, I identify four conformational states of the TMD that are associated with four types of packing between M2 helices. Packing in the extracellular half of the M2 helix produces closed conformations, while packing in the intracellular half produces both open and closed conformations. State transition is observed and supports a mechanism where iris-like twisting of the M2 helices switches the location of helical packing between the extracellular and the intracellular halves of the helices. In addition, this twisting motion alters the position and orientation of residue side-chains relative to the pore and therefore influences the pore geometry and possibly ion permeation. Helical packing, on the other hand, may restrict the twisting motion and generate discrete conformational states.
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18
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Niemann MCE, Weber H, Hluska T, Leonte G, Anderson SM, Novák O, Senes A, Werner T. The Cytokinin Oxidase/Dehydrogenase CKX1 Is a Membrane-Bound Protein Requiring Homooligomerization in the Endoplasmic Reticulum for Its Cellular Activity. PLANT PHYSIOLOGY 2018; 176:2024-2039. [PMID: 29301955 PMCID: PMC5841711 DOI: 10.1104/pp.17.00925] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/29/2017] [Indexed: 05/05/2023]
Abstract
Degradation of the plant hormone cytokinin is controlled by cytokinin oxidase/dehydrogenase (CKX) enzymes. The molecular and cellular behavior of these proteins is still largely unknown. In this study, we show that CKX1 is a type II single-pass membrane protein that localizes predominantly to the endoplasmic reticulum (ER) in Arabidopsis (Arabidopsis thaliana). This indicates that this CKX isoform is a bona fide ER protein directly controlling the cytokinin, which triggers the signaling from the ER. By using various approaches, we demonstrate that CKX1 forms homodimers and homooligomers in vivo. The amino-terminal part of CKX1 was necessary and sufficient for the protein oligomerization as well as for targeting and retention in the ER. Moreover, we show that protein-protein interaction is largely facilitated by transmembrane helices and depends on a functional GxxxG-like interaction motif. Importantly, mutations rendering CKX1 monomeric interfere with its steady-state localization in the ER and cause a loss of the CKX1 biological activity by increasing its ER-associated degradation. Therefore, our study provides evidence that oligomerization is a crucial parameter regulating CKX1 biological activity and the cytokinin concentration in the ER. The work also lends strong support for the cytokinin signaling from the ER and for the functional relevance of the cytokinin pool in this compartment.
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Affiliation(s)
- Michael C E Niemann
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Henriette Weber
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Tomáš Hluska
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, 78371 Olomouc, Czech Republic
| | - Georgeta Leonte
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Samantha M Anderson
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany ASCR, 78371 Olomouc, Czech Republic
| | - Alessandro Senes
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Tomáš Werner
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany ASCR, 78371 Olomouc, Czech Republic
- Institute of Plant Sciences, University of Graz, 8010 Graz, Austria
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19
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Koehler Leman J, D'Avino AR, Bhatnagar Y, Gray JJ. Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality. Proteins 2017; 86:57-74. [PMID: 29044728 DOI: 10.1002/prot.25402] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/27/2017] [Accepted: 10/11/2017] [Indexed: 12/29/2022]
Abstract
Membrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is "which structure is most biologically relevant?" Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X-ray crystallography. By investigating differences between the structures, we found that RMSDs between crystal and NMR structures are below 5 Å in the membrane region, NMR ensembles have a higher convergence in the membrane region, crystal structures typically have a straighter transmembrane region, have higher stereo-chemical correctness, and are more tightly packed. After quantifying these differences, we used high-resolution refinement of the NMR structures to mitigate them, which paves the way for identifying and improving the structural quality of membrane proteins.
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Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.,Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York
| | - Andrew R D'Avino
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.,Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Yash Bhatnagar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
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20
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Hu Z, Ho JC, Nallani M. Synthetic (polymer) biology (membrane): functionalization of polymer scaffolds for membrane proteins. Curr Opin Biotechnol 2017; 46:51-56. [DOI: 10.1016/j.copbio.2016.10.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/24/2016] [Indexed: 12/13/2022]
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21
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Hu T, Chen C, Li H, Dou Y, Zhou M, Lu D, Zong Q, Li Y, Yang C, Zhong Z, Singh N, Hu H, Zhang R, Yang H, Su D. Structural basis for dimerization and RNA binding of avian infectious bronchitis virus nsp9. Protein Sci 2017; 26:1037-1048. [PMID: 28257598 PMCID: PMC5405427 DOI: 10.1002/pro.3150] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/28/2017] [Accepted: 02/28/2017] [Indexed: 02/05/2023]
Abstract
The potential for infection by coronaviruses (CoVs) has become a serious concern with the recent emergence of Middle East respiratory syndrome and severe acute respiratory syndrome (SARS) in the human population. CoVs encode two large polyproteins, which are then processed into 15–16 nonstructural proteins (nsps) that make significant contributions to viral replication and transcription by assembling the RNA replicase complex. Among them, nsp9 plays an essential role in viral replication by forming a homodimer that binds single‐stranded RNA. Thus, disrupting nsp9 dimerization is a potential anti‐CoV therapy. However, different nsp9 dimer forms have been reported for alpha‐ and beta‐CoVs, and no structural information is available for gamma‐CoVs. Here we determined the crystal structure of nsp9 from the avian infectious bronchitis virus (IBV), a representative gamma‐CoV that affects the economy of the poultry industry because it can infect domestic fowl. IBV nsp9 forms a homodimer via interactions across a hydrophobic interface, which consists of two parallel alpha helices near the carboxy terminus of the protein. The IBV nsp9 dimer resembles that of SARS‐CoV nsp9, indicating that this type of dimerization is conserved among all CoVs. This makes disruption of the dimeric interface an excellent strategy for developing anti‐CoV therapies. To facilitate this effort, we characterized the roles of six conserved residues on this interface using site‐directed mutagenesis and a multitude of biochemical and biophysical methods. We found that three residues are critical for nsp9 dimerization and its abitlity to bind RNA. PDB Code(s): 5C94
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Affiliation(s)
- Tingting Hu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin, 300072, P.R. China
| | - Huiyan Li
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Yanshu Dou
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Ming Zhou
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Deren Lu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Qi Zong
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Yulei Li
- Department of Organic Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, P.R. China
| | - Cheng Yang
- College of Chemistry, Sichuan University, Chengdu, 610041, P.R. China
| | - Zhihui Zhong
- Laboratory of Non-human Primate Disease Modeling Research, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Namit Singh
- Ludwig Institute for Cancer Research, University of California, La Jolla, San Diego, California, 92093, USA
| | - Honggang Hu
- Department of Organic Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, P.R. China
| | - Rundong Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Haitao Yang
- School of Life Sciences, Tianjin University, Tianjin, 300072, P.R. China
| | - Dan Su
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
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22
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Steindorf D, Schneider D. In vivo selection of heterotypically interacting transmembrane helices: Complementary helix surfaces, rather than conserved interaction motifs, drive formation of transmembrane hetero-dimers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:245-256. [DOI: 10.1016/j.bbamem.2016.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 11/16/2022]
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23
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Evidence for Amino Acid Snorkeling from a High-Resolution, In Vivo Analysis of Fis1 Tail-Anchor Insertion at the Mitochondrial Outer Membrane. Genetics 2016; 205:691-705. [PMID: 28007883 PMCID: PMC5289845 DOI: 10.1534/genetics.116.196428] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/12/2016] [Indexed: 01/03/2023] Open
Abstract
Proteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of the Saccharomyces cerevisiaeFis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus. Prompted by our global analysis, we subsequently analyzed the ability of individual Fis1p TA mutants to localize to mitochondria. Our findings suggest that the membrane-associated domain of the Fis1p TA may be bipartite in nature, and we encountered evidence that the positively charged patch at the carboxyl terminus of Fis1p is required for both membrane insertion and organelle specificity. Furthermore, lengthening or shortening of the Fis1p TA by up to three amino acids did not inhibit mitochondrial targeting, arguing against a model in which TA length directs insertion of TAs to distinct organelles. Most importantly, positively charged residues were more acceptable at several positions within the membrane-associated domain of the Fis1p TA than negatively charged residues. These findings, emerging from the first high-resolution analysis of an organelle targeting sequence by deep mutational scanning, provide strong, in vivo evidence that lysine and arginine can “snorkel,” or become stably incorporated within a lipid bilayer by placing terminal charges of their side chains at the membrane interface.
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24
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Shelar A, Bansal M. Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2804-2817. [PMID: 27521749 DOI: 10.1016/j.bbamem.2016.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 08/07/2016] [Indexed: 12/11/2022]
Abstract
Transmembrane (TM) helices in integral membrane proteins are primarily α-helical in structure. Here we analyze 1134 TM helices in 90 high resolution membrane proteins and find that apart from the widely prevalent α-helices, TM regions also contain stretches of 310 (3 to 8 residues) and π-helices (5 to 19 residues) with distinct sequence signatures. The various helix perturbations in TM regions comprise of helices with kinked geometry, as well as those with an interspersed 310/π-helical fragment and show high occurrence in a few membrane proteins. Proline is frequently present at sites of these perturbations, but it is neither a necessary nor a sufficient requirement. Helix perturbations are also conserved within a family of membrane proteins despite low sequence identity in the perturbed region. Furthermore, a perturbation influences the geometry of the TM helix, mediates inter-helical interactions within and across protein chains and avoids hydrophobic mismatch of the helix termini with the bilayer. An analysis of π-helices in the TM regions of the heme copper oxidase superfamily shows that interspersed π-helices can vary in length from 6 to 19 amino acids or be entirely absent, depending upon the protein function. The results presented here would be helpful for prediction of 310 and π-helices in TM regions and can assist the computational design of membrane proteins.
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Affiliation(s)
- Ashish Shelar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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25
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Ng DP, Deber CM. Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues. Biochemistry 2016; 55:4306-15. [DOI: 10.1021/acs.biochem.6b00380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Derek P. Ng
- Department
of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
- Institute
of Medical Science, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
- Department
of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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26
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Li B, Mendenhall J, Nguyen ED, Weiner BE, Fischer AW, Meiler J. Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. J Chem Inf Model 2016; 56:423-34. [PMID: 26804342 PMCID: PMC5537626 DOI: 10.1021/acs.jcim.5b00517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prediction of the three-dimensional (3D) structures of proteins by computational methods is acknowledged as an unsolved problem. Accurate prediction of important structural characteristics such as contact number is expected to accelerate the otherwise slow progress being made in the prediction of 3D structure of proteins. Here, we present a dropout neural network-based method, TMH-Expo, for predicting the contact number of transmembrane helix (TMH) residues from sequence. Neuronal dropout is a strategy where certain neurons of the network are excluded from back-propagation to prevent co-adaptation of hidden-layer neurons. By using neuronal dropout, overfitting was significantly reduced and performance was noticeably improved. For multi-spanning helical membrane proteins, TMH-Expo achieved a remarkable Pearson correlation coefficient of 0.69 between predicted and experimental values and a mean absolute error of only 1.68. In addition, among those membrane protein-membrane protein interface residues, 76.8% were correctly predicted. Mapping of predicted contact numbers onto structures indicates that contact numbers predicted by TMH-Expo reflect the exposure patterns of TMHs and reveal membrane protein-membrane protein interfaces, reinforcing the potential of predicted contact numbers to be used as restraints for 3D structure prediction and protein-protein docking. TMH-Expo can be accessed via a Web server at www.meilerlab.org .
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Affiliation(s)
- Bian Li
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeffrey Mendenhall
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Elizabeth Dong Nguyen
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Brian E. Weiner
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Axel W. Fischer
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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Supunyabut C, Fuklang S, Sompornpisut P. Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane. J Mol Graph Model 2015; 59:81-91. [DOI: 10.1016/j.jmgm.2015.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/08/2023]
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Solution NMR Structure Determination of Polytopic α-Helical Membrane Proteins: A Guide to Spin Label Paramagnetic Relaxation Enhancement Restraints. Methods Enzymol 2015; 557:329-48. [PMID: 25950972 DOI: 10.1016/bs.mie.2014.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Solution nuclear magnetic resonance structures of polytopic α-helical membrane proteins require additional restraints beyond the traditional Nuclear Overhauser Effect (NOE) restraints. Several methods have been developed and this review focuses on paramagnetic relaxation enhancement (PRE). Important aspects of spin labeling, PRE measurements, structure calculations, and structural quality are discussed.
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The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions. Structure 2015; 23:527-541. [PMID: 25703378 DOI: 10.1016/j.str.2015.01.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/17/2014] [Accepted: 01/06/2015] [Indexed: 12/25/2022]
Abstract
α Helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of similar folds with various interhelical distances. The composition of the residues that pack at the interface between corresponding motifs shows that hydrophobic residues tend to be more enriched in the water-soluble class of structures and small residues in the transmembrane class. The latter group facilitates packing via sidechain- and backbone-mediated hydrogen bonds within the low-dielectric membrane milieu. The helix-helix interactome space, with its associated sequence preferences and accompanying hydrogen-bonding patterns, should be useful for engineering, prediction, and design of protein structure.
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Klein N, Neumann J, O'Neil JD, Schneider D. Folding and stability of the aquaglyceroporin GlpF: Implications for human aqua(glycero)porin diseases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:622-33. [PMID: 25462169 DOI: 10.1016/j.bbamem.2014.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 01/22/2023]
Abstract
Aquaporins are highly selective polytopic transmembrane channel proteins that facilitate the permeation of water across cellular membranes in a large diversity of organisms. Defects in aquaporin function are associated with common diseases, such as nephrogenic diabetes insipidus, congenital cataract and certain types of cancer. In general, aquaporins have a highly conserved structure; from prokaryotes to humans. The conserved structure, together with structural dynamics and the structural framework for substrate selectivity is discussed. The folding pathway of aquaporins has been a topic of several studies in recent years. These studies revealed that a conserved protein structure can be reached by following different folding pathways. Based on the available data, we suggest a complex folding pathway for aquaporins, starting from the insertion of individual helices up to the formation of the tetrameric aquaporin structure. The consequences of some known mutations in human aquaporin-encoding genes, which most likely affect the folding and stability of human aquaporins, are discussed.
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Affiliation(s)
- Noreen Klein
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Jennifer Neumann
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Joe D O'Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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31
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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32
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Ng DP, Deber CM. Terminal residue hydrophobicity modulates transmembrane helix-helix interactions. Biochemistry 2014; 53:3747-57. [PMID: 24857611 DOI: 10.1021/bi500317h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Central to the formation of tertiary structure in membrane protein folding is the presence of amino acid sequence motifs (such as "small-XXX-small" segments) in the TM segments that promote interaction-compatible surfaces through which the TM α-helices interact. Here, we sought to elucidate additional factors that may work in tandem to dictate the ultimate interaction fate of TM-embedded segments. In this context, we used proteolipid protein (PLP), the major protein from central nervous system myelin for which mutant-dependent non-native oligomerization has been implicated in neurological disorders, to explore the specific effects of TM boundary residues (the membrane entry and exit points), keying on the secondary structure and self-association of peptides corresponding to the PLP TM2 α-helix (wild-type sequence ⁶⁶AFQYVIYGTASFFFLYGALLLAEGF⁹⁰). Using gel electrophoresis, circular dichroism, and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate (SDS), we found that mutation of F90 to residues such as A, I, L, or V maintains the onset of TM2-TM2 dimerization, whereas mutation to E, G, Q, N, S, or T abrogates dimer formation. We attribute this sensitivity to changes in local hydrophobicity, viz., a decrease in hydrophobicity reduces local lipid-peptide interactions, which in turn disrupts peptide α-helicity and hence the effectiveness of an incipient interaction-compatible surface. Our results show that the secondary structure and oligomeric state of PLP TM2 Lys-tagged peptides are significantly modulated by the specific nature of their C-terminal boundary residue, thus providing insight as to how point mutations, particularly where they produce disease states, can compromise the folding process.
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Affiliation(s)
- Derek P Ng
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children , Toronto, Ontario M5G 0A4, Canada
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33
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Saravanan K, Krishnaswamy S. Analysis of dihedral angle preferences for alanine and glycine residues in alpha and beta transmembrane regions. J Biomol Struct Dyn 2014; 33:552-62. [DOI: 10.1080/07391102.2014.895678] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Probabilistic grammatical model for helix-helix contact site classification. Algorithms Mol Biol 2013; 8:31. [PMID: 24350601 PMCID: PMC3892132 DOI: 10.1186/1748-7188-8-31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 11/28/2013] [Indexed: 11/25/2022] Open
Abstract
Background Hidden Markov Models power many state‐of‐the‐art tools in
the field of protein bioinformatics. While excelling in their tasks, these
methods of protein analysis do not convey directly information on
medium‐ and long‐range residue‐residue interactions. This
requires an expressive power of at least context‐free grammars.
However, application of more powerful grammar formalisms to protein analysis
has been surprisingly limited. Results In this work, we present a probabilistic grammatical framework for
problem‐specific protein languages and apply it to classification of
transmembrane helix‐helix pairs configurations. The core of the model
consists of a probabilistic context‐free grammar, automatically
inferred by a genetic algorithm from only a generic set of
expert‐based rules and positive training samples. The model was
applied to produce sequence based descriptors of four classes of
transmembrane helix‐helix contact site configurations. The highest
performance of the classifiers reached AUCROC of 0.70. The analysis of grammar parse trees revealed the ability
of representing structural features of helix‐helix contact sites. Conclusions We demonstrated that our probabilistic context‐free framework for
analysis of protein sequences outperforms the state of the art in the task
of helix‐helix contact site classification. However, this is achieved
without necessarily requiring modeling long range dependencies between
interacting residues. A significant feature of our approach is that grammar
rules and parse trees are human‐readable. Thus they could provide
biologically meaningful information for molecular biologists.
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35
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Rose A, Theune D, Goede A, Hildebrand PW. MP:PD--a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins. Nucleic Acids Res 2013; 42:D347-51. [PMID: 24194596 PMCID: PMC3965053 DOI: 10.1093/nar/gkt1062] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The membrane protein packing database (MP:PD) (http://proteinformatics.charite.de/mppd) is a database of helical membrane proteins featuring internal atomic packing densities, cavities and waters. Membrane proteins are not tightly packed but contain a considerable number of internal cavities that differ in volume, polarity and solvent accessibility as well as in their filling with internal water. Internal cavities are supposed to be regions of high physical compressibility. By serving as mobile hydrogen bonding donors or acceptors, internal waters likely facilitate transition between different functional states. Despite these distinct functional roles, internal cavities of helical membrane proteins are not well characterized, mainly because most internal waters are not resolved by crystal structure analysis. Here we combined various computational biophysical techniques to characterize internal cavities, reassign positions of internal waters and calculate internal packing densities of all available helical membrane protein structures and stored them in MP:PD. The database can be searched using keywords and entries can be downloaded. Each entry can be visualized in Provi, a Jmol-based protein viewer that provides an integrated display of low energy waters alongside membrane planes, internal packing density, hydrophobic cavities and hydrogen bonds.
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Affiliation(s)
- Alexander Rose
- Charité University Medicine Berlin, Institute of Medical Physics and Biophysics, ProteinFormatics Group, Charitéplatz 1, 10117 Berlin and Charité University Medicine Berlin, Institute for Physiology, Structural Bioinformatics Group, Lindenberger Weg 80, 13125 Berlin
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36
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Benjamini A, Smit B. Robust driving forces for transmembrane helix packing. Biophys J 2013; 103:1227-35. [PMID: 22995495 DOI: 10.1016/j.bpj.2012.08.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022] Open
Abstract
The packing structures of transmembrane helices are traditionally attributed to patterns in residues along the contact surface. In this view, besides keeping the helices confined in the membrane, the bilayer has only a minor effect on the helices structure. Here, we use two different approaches to show that the lipid environment has a crucial effect in determining the cross-angle distribution of packed helices. We analyzed structural data of a membrane proteins database. We show that the distribution of cross angles of helix pairs in this database is statistically indistinguishable from the cross-angle distribution of two noninteracting helices imbedded in the membrane. These results suggest that the cross angle is, to a large extent, determined by the tilt angle of the individual helices. We test this hypothesis using molecular simulations of a coarse-grained model that contains no specific residue interactions. These simulations reproduce the same cross-angle distribution as found in the database. As the tilt angle of a helix is dominated by hydrophobic mismatch between the protein and surrounding lipids, our results indicate that hydrophobic mismatch is the dominant factor guiding the transmembrane helix packing. Other short-range forces might then fine-tune the structure to its final configuration.
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Affiliation(s)
- Ayelet Benjamini
- Department of Chemistry, University of California, Berkeley, California, USA
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Abstract
Of great interest to the academic and pharmaceutical research communities, helical transmembrane proteins are characterized by their ability to dissolve and fold in lipid bilayers—properties conferred by polypeptide spans termed transmembrane domains (TMDs). The apolar nature of TMDs necessitates the use of membrane-mimetic solvents for many structure and folding studies. This review examines the relationship between TMD structure and solvent environment, focusing on principles elucidated largely in membrane-mimetic environments with single-TMD protein and peptide models. Following a brief description of TMD sequence and conformational characteristics gleaned from the structural database, we present an overview of the conceptual models used to study folding in vitro. The impact of sequence and solvent context on the incorporation of TMDs into membranes, and its role in measurements of TMD self-assembly strengths, is then described. We conclude with a discussion of the nonspecific effects of membrane components on TMD stability.
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Affiliation(s)
- Arianna Rath
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
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38
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Joo H, Chavan AG, Phan J, Day R, Tsai J. An amino acid packing code for α-helical structure and protein design. J Mol Biol 2012; 419:234-54. [PMID: 22426125 DOI: 10.1016/j.jmb.2012.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/22/2012] [Accepted: 03/07/2012] [Indexed: 11/19/2022]
Abstract
This work demonstrates that all packing in α-helices can be simplified to repetitive patterns of a single motif: the knob-socket. Using the precision of Voronoi Polyhedra/Delauney Tessellations to identify contacts, the knob-socket is a four-residue tetrahedral motif: a knob residue on one α-helix packs into the three-residue socket on another α-helix. The principle of the knob-socket model relates the packing between levels of protein structure: the intra-helical packing arrangements within secondary structure that permit inter-helix tertiary packing interactions. Within an α-helix, the three-residue sockets arrange residues into a uniform packing lattice. Inter-helix packing results from a definable pattern of interdigitated knob-socket motifs between two α-helices. Furthermore, the knob-socket model classifies three types of sockets: (1) free, favoring only intra-helical packing; (2) filled, favoring inter-helical interactions; and (3) non, disfavoring α-helical structure. The amino acid propensities in these three socket classes essentially represent an amino acid code for structure in α-helical packing. Using this code, we used a novel yet straightforward approach for the design of α-helical structure to validate the knob-socket model. Unique sequences for three peptides were created to produce a predicted amount of α-helical structure: mostly helical, some helical, and no helix. These three peptides were synthesized, and helical content was assessed using CD spectroscopy. The measured α-helicity of each peptide was consistent with the expected predictions. These results and analysis demonstrate that the knob-socket motif functions as the basic unit of packing and presents an intuitive tool to decipher the rules governing packing in protein structure.
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Affiliation(s)
- Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA
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39
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Liu L, Ivanov AV, Gable ME, Jolivel F, Morrill GA, Askari A. Comparative properties of caveolar and noncaveolar preparations of kidney Na+/K+-ATPase. Biochemistry 2011; 50:8664-73. [PMID: 21905705 PMCID: PMC3186040 DOI: 10.1021/bi2009008] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
To evaluate previously proposed functions of renal caveolar
Na+/K+-ATPase, we modified the standard procedures
for the preparation of the purified membrane-bound kidney enzyme,
separated the caveolar and noncaveolar pools, and compared their properties.
While the subunits of Na+/K+-ATPase (α,β,γ)
constituted most of the protein content of the noncaveolar pool, the
caveolar pool also contained caveolins and major caveolar proteins
annexin-2 tetramer and E-cadherin. Ouabain-sensitive Na+/K+-ATPase activities of the two pools had similar properties
and equal molar activities, indicating that the caveolar enzyme retains
its ion transport function and does not contain nonpumping enzyme.
As minor constituents, both caveolar and noncaveolar pools also contained
Src, EGFR, PI3K, and several other proteins known to be involved in
stimulous-induced signaling by Na+/K+-ATPase,
indicating that signaling function is not limited to the caveolar
pool. Endogenous Src was active in both pools but was not further
activated by ouabain, calling into question direct interaction of
Src with native Na+/K+-ATPase. Chemical cross-linking,
co-immunoprecipitation, and immunodetection studies showed that in
the caveolar pool, caveolin-1 oligomers, annexin-2 tetramers, and
oligomers of the α,β,γ-protomers of Na+/K+-ATPase form a large multiprotein complex. In conjunction
with known roles of E-cadherin and the β-subunit of Na+/K+-ATPase in cell adhesion and noted intercellular β,β-contacts
within the structure of Na+/K+-ATPase, our findings
suggest that interacting caveolar Na+/K+-ATPases
located at renal adherens junctions maintain contact of two adjacent
cells, conduct essential ion pumping, and are capable of locus-specific
signaling in junctional cells.
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Affiliation(s)
- Lijun Liu
- Department of Biochemistry and Cancer Biology, University of Toledo Health Science Campus, Toledo, Ohio 43614, United States
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40
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Kitazoe Y, Kishino H, Hasegawa M, Matsui A, Lane N, Tanaka M. Stability of mitochondrial membrane proteins in terrestrial vertebrates predicts aerobic capacity and longevity. Genome Biol Evol 2011; 3:1233-44. [PMID: 21824868 PMCID: PMC3227407 DOI: 10.1093/gbe/evr079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The cellular energy produced by mitochondria is a fundamental currency of life. However, the extent to which mitochondrial (mt) performance (power and endurance) is adapted to habitats and life strategies of vertebrates is not well understood. A global analysis of mt genomes revealed that hydrophobicity (HYD) of mt membrane proteins (MMPs) is much lower in terrestrial vertebrates than in fishes and shows a strong negative correlation with serine/threonine composition (STC). Here, we present evidence that this systematic feature of MMPs was crucial for the evolution of large terrestrial vertebrates with high aerobic capacity. An Arrhenius-type equation gave positive correlations between STC and maximum life span (MLS) in terrestrial vertebrates (with a few exceptions relating to the lifestyle of small animals with a high resting metabolic rate [RMR]) and negative correlations in secondary marine vertebrates, such as cetaceans and alligators (which returned from land to water, utilizing buoyancy with increased body size). In particular, marked STC increases in primates (especially hominoids) among placentals were associated with very high MLS values. We connected these STC increases in MMPs with greater stability of respiratory complexes by estimating the degradation of the Arrhenius plot given by accelerating mtRMR up to mt maximum metabolic rate. Both mtRMR and HYD in terrestrial vertebrates decreased with increasing body mass. Decreases in mtRMR raise MMP stability when high mobility is not required, whereas decreased HYD may weaken this stability under the hydrophobic environment of lipid bilayer. High maximal metabolic rates (5–10 RMR), which we postulate require high MMP mobility, presumably render MMPs more unstable. A marked rise in STC may therefore be essential to stabilize MMPs, perhaps as dynamic supercomplexes, via hydrogen bonds associated with serine/threonine motifs.
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Affiliation(s)
- Yasuhiro Kitazoe
- Center of Medical Information Science, Kochi Medical School, Nankoku, Kochi, Japan.
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41
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Hedin LE, Illergård K, Elofsson A. An Introduction to Membrane Proteins. J Proteome Res 2011; 10:3324-31. [DOI: 10.1021/pr200145a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Linnea E. Hedin
- Department of Biochemitry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Science for life laboratory, Swedish E-science Research Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Kristoffer Illergård
- Department of Biochemitry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Science for life laboratory, Swedish E-science Research Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Arne Elofsson
- Department of Biochemitry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Science for life laboratory, Swedish E-science Research Center, Stockholm University, 106 91 Stockholm, Sweden
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42
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Meruelo AD, Samish I, Bowie JU. TMKink: a method to predict transmembrane helix kinks. Protein Sci 2011; 20:1256-64. [PMID: 21563225 DOI: 10.1002/pro.653] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/22/2011] [Indexed: 01/24/2023]
Abstract
A hallmark of membrane protein structure is the large number of distorted transmembrane helices. Because of the prevalence of bends, it is important to not only understand how they are generated but also to learn how to predict their occurrence. Here, we find that there are local sequence preferences in kinked helices, most notably a higher abundance of proline, which can be exploited to identify bends from local sequence information. A neural network predictor identifies over two-thirds of all bends (sensitivity 0.70) with high reliability (specificity 0.89). It is likely that more structural data will allow for better helix distortion predictors with increased coverage in the future. The kink predictor, TMKink, is available at http://tmkinkpredictor.mbi.ucla.edu/.
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Affiliation(s)
- Alejandro D Meruelo
- Medical Scientist Training Program, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1570, USA
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43
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Lo A, Cheng CW, Chiu YY, Sung TY, Hsu WL. TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. Nucleic Acids Res 2011; 39:D347-55. [PMID: 21177659 PMCID: PMC3013749 DOI: 10.1093/nar/gkq1255] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
α-Helical transmembrane (TM) proteins play an important role in many critical and diverse biological processes, and specific associations between TM helices are important determinants for membrane protein folding, dynamics and function. In order to gain insights into the above phenomena, it is necessary to investigate different types of helix-packing modes and interactions. However, such information is difficult to obtain because of the experimental impediment and a lack of a well-annotated source of helix-packing folds in TM proteins. We have developed the TMPad (TransMembrane Protein Helix-Packing Database) which addresses the above issues by integrating experimentally observed helix–helix interactions and related structural information of membrane proteins. Specifically, the TMPad offers pre-calculated geometric descriptors at the helix-packing interface including residue backbone/side-chain contacts, interhelical distances and crossing angles, helical translational shifts and rotational angles. The TMPad also includes the corresponding sequence, topology, lipid accessibility, ligand-binding information and supports structural classification, schematic diagrams and visualization of the above structural features of TM helix-packing. Through detailed annotations and visualizations of helix-packing, this online resource can serve as an information gateway for deciphering the relationship between helix–helix interactions and higher levels of organization in TM protein structure and function. The website of the TMPad is freely accessible to the public at http://bio-cluster.iis.sinica.edu.tw/TMPad.
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Affiliation(s)
- Allan Lo
- Bioinformatics Laboratory, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan, Republic of China
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Hayat S, Park Y, Helms V. Statistical analysis and exposure status classification of transmembrane beta barrel residues. Comput Biol Chem 2011; 35:96-107. [PMID: 21531175 DOI: 10.1016/j.compbiolchem.2011.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 03/01/2011] [Accepted: 03/01/2011] [Indexed: 12/28/2022]
Abstract
Several computational methods exist for the identification of transmembrane beta barrel proteins (TMBs) from sequence. Some of these methods also provide the transmembrane (TM) boundaries of the putative TMBs. The aim of this study is to (1) derive the propensities of the TM residues to be exposed to the lipid bilayer and (2) to predict the exposure status (i.e. exposed to the bilayer or hidden in protein structure) of TMB residues. Three novel propensity scales namely, BTMC, BTMI and HTMI were derived for the TMB residues at the hydrophobic core region of the outer membrane (OM), the lipid-water interface regions of the OM, and for the helical membrane proteins (HMPs) residues at the lipid-water interface regions of the inner membrane (IM), respectively. Separate propensity scales were derived for monomeric and functionally oligomeric TMBs. The derived propensities reflect differing physico-chemical properties of the respective membrane bilayer regions and were employed in a computational method for the prediction of the exposure status of TMB residues. Based on the these propensities, the conservation indices and the frequency profile of the residues, the transmembrane residues were classified into buried/exposed with an accuracy of 77.91% and 80.42% for the residues at the membrane core and the interface regions, respectively. The correlation of the derived scales with different physico-chemical properties obtained from the AAIndex database are also discussed. Knowledge about the residue propensities and burial status will be useful in annotating putative TMBs with unknown structure.
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Affiliation(s)
- Sikander Hayat
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
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Sodt AJ, Head-Gordon T. Driving forces for transmembrane alpha-helix oligomerization. Biophys J 2010; 99:227-37. [PMID: 20655851 DOI: 10.1016/j.bpj.2010.03.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 03/24/2010] [Accepted: 03/29/2010] [Indexed: 11/25/2022] Open
Abstract
We present what we believe to be a novel statistical contact potential based on solved structures of transmembrane (TM) alpha-helical bundles, and we use this contact potential to investigate the amino acid likelihood of stabilizing helix-helix interfaces. To increase statistical significance, we have reduced the full contact energy matrix to a four-flavor alphabet of amino acids, automatically determined by our methodology, in which we find that polarity is a more dominant factor of group identity than is size, with charged or polar groups most often occupying the same face, whereas polar/apolar residue pairs tend to occupy opposite faces. We found that the most polar residues strongly influence interhelical contact formation, although they occur rarely in TM helical bundles. Two-body contact energies in the reduced letter code are capable of determining native structure from a large decoy set for a majority of test TM proteins, at the same time illustrating that certain higher-order sequence correlations are necessary for more accurate structure predictions.
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Affiliation(s)
- Alex J Sodt
- Department of Bioengineering, University of California, Berkeley, California, USA.
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Monticelli L, Tieleman DP, Fuchs PF. Interpretation of 2H-NMR experiments on the orientation of the transmembrane helix WALP23 by computer simulations. Biophys J 2010; 99:1455-64. [PMID: 20816057 PMCID: PMC2931731 DOI: 10.1016/j.bpj.2010.05.039] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 05/17/2010] [Accepted: 05/21/2010] [Indexed: 01/11/2023] Open
Abstract
Orientation, dynamics, and packing of transmembrane helical peptides are important determinants of membrane protein structure, dynamics, and function. Because it is difficult to investigate these aspects by studying real membrane proteins, model transmembrane helical peptides are widely used. NMR experiments provide information on both orientation and dynamics of peptides, but they require that motional models be interpreted. Different motional models yield different interpretations of quadrupolar splittings (QS) in terms of helix orientation and dynamics. Here, we use coarse-grained (CG) molecular dynamics (MD) simulations to investigate the behavior of a well-known model transmembrane peptide, WALP23, under different hydrophobic matching/mismatching conditions. We compare experimental (2)H-NMR QS (directly measured in experiments), as well as helix tilt angle and azimuthal rotation (not directly measured), with CG MD simulation results. For QS, the agreement is significantly better than previously obtained with atomistic simulations, indicating that equilibrium sampling is more important than atomistic details for reproducing experimental QS. Calculations of helix orientation confirm that the interpretation of QS depends on the motional model used. Our simulations suggest that WALP23 can form dimers, which are more stable in an antiparallel arrangement. The origin of the preference for the antiparallel orientation lies not only in electrostatic interactions but also in better surface complementarity. In most cases, a mixture of monomers and antiparallel dimers provides better agreement with NMR data compared to the monomer and the parallel dimer. CG MD simulations allow predictions of helix orientation and dynamics and interpretation of QS data without requiring any assumption about the motional model.
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Affiliation(s)
- Luca Monticelli
- INSERM UMR-S 665, DSIMB, Paris, France
- Université Paris Diderot, UFR, Sciences du Vivant, Paris, France
- Institut National de Transfusion Sanguine, Paris, France
| | - D. Peter Tieleman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Patrick F.J. Fuchs
- INSERM UMR-S 665, DSIMB, Paris, France
- Université Paris Diderot, UFR, Sciences du Vivant, Paris, France
- Institut National de Transfusion Sanguine, Paris, France
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Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm. PLoS Comput Biol 2010; 6:e1000714. [PMID: 20333233 PMCID: PMC2841610 DOI: 10.1371/journal.pcbi.1000714] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 02/10/2010] [Indexed: 11/24/2022] Open
Abstract
Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/. Alpha-helical transmembrane proteins constitute a significant proportion of the proteins encoded in a typical genome and are involved in a wide variety of important biological processes. Many common diseases including diabetes, hypertension and epilepsy have been related to transmembrane protein dysfunction, therefore they represent one of the most important classes of protein for pharmaceutical intervention. However, due to the experimental difficulties of structure determination, this class of protein is severely under-represented in structural databases. Here, we present a novel approach that is able to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of a transmembrane protein. Under stringent cross-validation, our approach demonstrates a significant improvement in prediction over existing software. This method can be used to gain insights into transmembrane protein folding and enhance the quality of ab initio modelling, while providing testable hypotheses for a variety of studies including protein design, mutagenesis and thermostability experiments.
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Chugunov AO, Efremov RG. [Prediction of the spatial structure of proteins: emphasis on membrane targets]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 35:744-60. [PMID: 20208575 DOI: 10.1134/s106816200906003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Knowledge of the spatial structure of proteins is a prerequisite for both awareness of their functional mechanisms and the framework for rational drug discovery and design. Meanwhile, direct structural determination is often hampered or impractical due to the complexity, expensiveness, and limited capabilities of experimental techniques. These issues are especially pronounced for integral membrane proteins. On numerous occasions, the theoretical prediction of protein structures may facilitate the process by exploiting physical or empirical principles. This paper surveys modern techniques for the prediction of the spatial structure of proteins using computer algorithms, and the main emphasis is placed on the most "complex" targets - membrane proteins (MPs). The first part of the review describes de novo methods based on empirical physical principles; in the second part, a comparative modeling philosophy, which accounts for the structure of related proteins, is described. Special focus is made regarding pharmacologically relevant classes of G-coupled receptors, receptor tyrosine ki-nases, and other MPs. Algorithms for the assessment of the models quality and potential fields of application of computer models are discussed.
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Etchebest C, Debret G. Critical review of general guidelines for membrane proteins model building and analysis. Methods Mol Biol 2010; 654:363-385. [PMID: 20665276 DOI: 10.1007/978-1-60761-762-4_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Membrane proteins play major roles in many biological processes such as signalling, transport, etc. They have been shown to be involved in the development of many diseases and have become important drug targets per se. The understanding of their functional properties may be facilitated if a 3D structure is available. However, in the case of membrane proteins, only a few 3D structures have been solved to date. Bioinformatics and molecular modelling approaches are thus powerful alternatives to fill the gap between the sequence and the structure. Here, a review of the most recent approaches is proposed together with guidelines on how to use them. In addition, insofar as important biological processes require conformational changes, we discuss some interesting methods aimed at exploring the dynamic behaviour of proteins in their membrane environment. The paper ends with a brief description of useful approaches for determining oligomerisation or ligand binding sites.
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Affiliation(s)
- Catherine Etchebest
- INSERM UMR-S 665, Equipe Dynamique des Structures et des Interactions des Macromolécules Biologiques (DSIMB), Institut National de Transfusion Sanguine (INTS), Université Paris Diderot - Paris 7, Paris, France.
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Haeger S, Kuzmin D, Detro-Dassen S, Lang N, Kilb M, Tsetlin V, Betz H, Laube B, Schmalzing G. An intramembrane aromatic network determines pentameric assembly of Cys-loop receptors. Nat Struct Mol Biol 2009; 17:90-8. [PMID: 20023641 DOI: 10.1038/nsmb.1721] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Accepted: 10/19/2009] [Indexed: 12/28/2022]
Abstract
Cys-loop receptors are pentameric ligand-gated ion channels (pLGICs) that mediate fast synaptic transmission. Here functional pentameric assembly of truncated fragments comprising the ligand-binding N-terminal ectodomains and the first three transmembrane helices, M1-M3, of both the inhibitory glycine receptor (GlyR) alpha1 and the 5HT(3)A receptor subunits was found to be rescued by coexpressing the complementary fourth transmembrane helix, M4. Alanine scanning identified multiple aromatic residues in M1, M3 and M4 as key determinants of GlyR assembly. Homology modeling and molecular dynamics simulations revealed that these residues define an interhelical aromatic network, which we propose determines the geometry of M1-M4 tetrahelical packing such that nascent pLGIC subunits must adopt a closed fivefold symmetry. Because pLGIC ectodomains form random nonstoichiometric oligomers, proper pentameric assembly apparently depends on intersubunit interactions between extracellular domains and intrasubunit interactions between transmembrane segments.
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Affiliation(s)
- Svenja Haeger
- Molecular Pharmacology, RWTH Aachen University of Aachen, Aachen, Germany
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