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Corin K, Bowie JU. How physical forces drive the process of helical membrane protein folding. EMBO Rep 2022; 23:e53025. [PMID: 35133709 PMCID: PMC8892262 DOI: 10.15252/embr.202153025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/17/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Protein folding is a fundamental process of life with important implications throughout biology. Indeed, tens of thousands of mutations have been associated with diseases, and most of these mutations are believed to affect protein folding rather than function. Correct folding is also a key element of design. These factors have motivated decades of research on protein folding. Unfortunately, knowledge of membrane protein folding lags that of soluble proteins. This gap is partly caused by the greater technical challenges associated with membrane protein studies, but also because of additional complexities. While soluble proteins fold in a homogenous water environment, membrane proteins fold in a setting that ranges from bulk water to highly charged to apolar. Thus, the forces that drive folding vary in different regions of the protein, and this complexity needs to be incorporated into our understanding of the folding process. Here, we review our understanding of membrane protein folding biophysics. Despite the greater challenge, better model systems and new experimental techniques are starting to unravel the forces and pathways in membrane protein folding.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
| | - James U Bowie
- Department of Chemistry and BiochemistryMolecular Biology InstituteUCLA‐DOE InstituteUniversity of CaliforniaLos AngelesCAUSA
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2
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Baranowska-Łączkowska A, Banaszak-Piechowska A, Donarska B, Łączkowski KZ. Towards understanding the interaction of (S)-thalidomide with nucleobases. Arch Biochem Biophys 2020; 693:108566. [PMID: 32896516 DOI: 10.1016/j.abb.2020.108566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/16/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
Interaction of (S)-thalidomide molecule with four nucleobases: adenine, guanine, cytosine and thymine, is investigated in details employing density functional theory methods. Different mutual positions of the molecules are considered, with the starting geometries enabling hydrogen bond interactions between the monomers. Optimization of geometrical parameters is carried out within the B3LYP/6-311G** approximation and followed by evaluation of vibrational frequencies. Binding and interaction energies are calculated employing exchange-correlation functionals including long-range corrections and properly diffuse basis sets. The strongest interaction exists within the (S)-thalidomide-guanine complex. Interestingly, in one of the investigated (S)-thalidomide-guanine complexes two bifurcated hydrogen bonds are observed. The two hydrogens involved in one of them are bonded to a carbon atom in the α position relative to carbonyl group. The present study can be useful in the design of new anticancer and antiviral drugs interacting selectively with DNA or RNA.
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Affiliation(s)
| | | | - Beata Donarska
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum Nicolaus Copernicus University, 2 Jurasz St., PL-85089, Bydgoszcz, Poland
| | - Krzysztof Z Łączkowski
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum Nicolaus Copernicus University, 2 Jurasz St., PL-85089, Bydgoszcz, Poland.
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3
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Dhar J, Chakrabarti P, Saini H, Raghava GPS, Kishore R. ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction. Proteins 2014; 83:203-14. [PMID: 25388861 DOI: 10.1002/prot.24720] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/28/2014] [Accepted: 11/03/2014] [Indexed: 11/10/2022]
Abstract
Mimicry of structural motifs is a common feature in proteins. The 10-membered hydrogen-bonded ring involving the main-chain C − O in a β-turn can be formed using a side-chain carbonyl group leading to Asx-turn. We show that the N − H component of hydrogen bond can be replaced by a C(γ) -H group in the side chain, culminating in a nonconventional C − H···O interaction. Because of its shape this β-turn mimic is designated as ω-turn, which is found to occur ∼ three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C − H···O interaction occurring between the terminal residues, constraining the torsion angles ϕi + 1, ψi + 1, ϕi + 2 and χ'1(i + 2) (using the interacting C(γ) atom). Based on these angles there are two types of ω-turns, each of which can be further divided into two groups. C(β) -branched side-chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal-binding sites. N-linked glycosylation occurs at the consensus pattern Asn-Xaa-Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω-turn, which may be the recognition site for protein modification. Location between two β-strands is the most common occurrence in protein tertiary structure, and being generally exposed ω-turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design.
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Affiliation(s)
- Jesmita Dhar
- Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, 700 054, India
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4
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Bhadbhade MM, Kishore R. Intramolecular CH···O Hydrogen-bond mediated stabilization of a Cis-DPro imide-bond in a stereocontrolled heterochiral model peptide. Biopolymers 2011; 97:73-82. [DOI: 10.1002/bip.21705] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 07/21/2011] [Indexed: 11/06/2022]
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5
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Magnuson A, Krassen H, Stensjö K, Ho FM, Styring S. Modeling Photosystem I with the alternative reaction center protein PsaB2 in the nitrogen fixing cyanobacterium Nostoc punctiforme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1152-61. [PMID: 21605545 DOI: 10.1016/j.bbabio.2011.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 04/21/2011] [Accepted: 05/07/2011] [Indexed: 11/18/2022]
Abstract
Five nitrogen fixing cyanobacterial strains have been found to contain PsaB2, an additional and divergent gene copy for the Photosystem I reaction center protein PsaB. In all five species the divergent gene, psaB2, is located separately from the normal psaAB operon in the genome. The protein, PsaB2, was recently identified in heterocysts of Nostoc punctiforme sp. strain PCC 73102. 12 conserved amino acid replacements and one insertion, were identified by a multiple sequence alignment of several PsaB2 and PsaB1 sequences. Several, including an inserted glutamine, are located close to the iron-sulfur cluster F(X) in the electron transfer chain. By homology modeling, using the Photosystem I crystal structure as template, we have found that the amino acid composition in PsaB2 will introduce changes in critical parts of the Photosystem I protein structure. The changes are close to F(X) and the phylloquinone (PhQ) in the B-branch, indicating that the electron transfer properties most likely will be affected. We suggest that the divergent PsaB2 protein produces an alternative Photosystem I reaction center with different structural and electron transfer properties. Some interesting physiologcial consequences that this can have for the function of Photosystem I in heterocysts, are discussed.
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Affiliation(s)
- Ann Magnuson
- Department of Photochemistryand Molecular Science, Uppsala University, Sweden.
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6
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Laungani A, Keller M, Slattery J, Krossing I, Breit B. Cooperative Effect of a Classical and a Weak Hydrogen Bond for the Metal-Induced Construction of a Self-Assembled β-Turn Mimic. Chemistry 2009; 15:10405-22. [DOI: 10.1002/chem.200900662] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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7
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Otero Areán C. Dinitrogen and carbon monoxide hydrogen bonding in protonic zeolites: Studies from variable-temperature infrared spectroscopy. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Uldry AC, Griffin JM, Yates JR, Pérez-Torralba M, Santa María MD, Webber AL, Beaumont MLL, Samoson A, Claramunt RM, Pickard CJ, Brown SP. Quantifying Weak Hydrogen Bonding in Uracil and 4-Cyano-4‘-ethynylbiphenyl: A Combined Computational and Experimental Investigation of NMR Chemical Shifts in the Solid State. J Am Chem Soc 2008; 130:945-54. [DOI: 10.1021/ja075892i] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Anne-Christine Uldry
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - John M. Griffin
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Jonathan R. Yates
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Marta Pérez-Torralba
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - M. Dolores Santa María
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Amy L. Webber
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Maximus L. L. Beaumont
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Ago Samoson
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Rosa María Claramunt
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Chris J. Pickard
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Steven P. Brown
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
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9
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Scheiner S. Contributions of NH...O and CH...O hydrogen bonds to the stability of beta-sheets in proteins. J Phys Chem B 2007; 110:18670-9. [PMID: 16970498 DOI: 10.1021/jp063225q] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ab initio quantum calculations are applied to both the parallel and the antiparallel arrangements of the beta-sheets of proteins. The energies of the NH...O and CH...O hydrogen bonds present in the beta-sheet are evaluated separately from one another by appropriate modifications of the model systems. The bond energies of these two sorts of hydrogen bonds are found to be very nearly equal in the parallel beta-sheet. The NH...O bonds are stronger than CH...O in the antiparallel geometry but only by a relatively small margin. Moreover, the former NH...O bonds are weakened when placed next to one another, as occurs in the antiparallel beta-sheet. As a result, there is little energetic distinction between the NH...O and CH...O bonds in the full antiparallel beta-sheet, just as in the parallel structure.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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10
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Scheiner S. Relative strengths of NH..O and CH..O hydrogen bonds between polypeptide chain segments. J Phys Chem B 2007; 109:16132-41. [PMID: 16853050 DOI: 10.1021/jp053416d] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Correlated ab initio calculations are used to compare the energetics when the CH and NH groups of the model dipeptide CHONHCH2CONH2 are each allowed to form a H-bond with the proton acceptor O of a peptide group. When the dipeptide is in its C7 conformation, the NH..O H-bond energy is found to be 7.4 kcal/mol, as compared to only 2.8 kcal/mol for the CH..O interaction. On the other hand, the situation reverses, and the CH..O H-bond becomes stronger than NH..O, when the dipeptide adopts a C5 structure. This reversal is important as C5 is nearly equal in stability to C7 for the dipeptide, and is representative of the commonly observed beta-sheet structure in a protein. Immersing the dipeptide-peptide pair in a model solvent weakens both sorts of H-bonds, and in a fairly uniform manner. Consequently, the trends observed in the in vacuo situation retain their validity in either aqueous solution or the protein interior. Likewise, the desolvation penalty, suffered by removing a H-bonded complex from water and placing it in the less polar interior of a protein, is quite similar for the NH..O and CH..O bonds.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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11
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Chakrabarti P, Bhattacharyya R. Geometry of nonbonded interactions involving planar groups in proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2007; 95:83-137. [PMID: 17629549 DOI: 10.1016/j.pbiomolbio.2007.03.016] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 03/18/2007] [Indexed: 11/26/2022]
Abstract
Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on the geometry of interaction between planar moieties of ten side chains (Phe, Tyr, Trp, His, Arg, Pro, Asp, Glu, Asn and Gln), the aromatic residues and the sulfide planes (of Met and cystine), and the aromatic residues and the peptide planes within the protein tertiary structures available in the Protein Data Bank. The occurrence of hydrogen bonds and other nonconventional interactions such as C-H...pi, C-H...O, electrophile-nucleophile interactions involving the planar moieties has been elucidated. The specific nature of the interactions constraints many of the residue pairs to occur with a fixed sequence difference, maintaining a sequential order, when located in secondary structural elements, such as alpha-helices and beta-turns. The importance of many of these interactions (for example, aromatic residues interacting with Pro or cystine sulfur atom) is revealed by the higher degree of conservation observed for them in protein structures and binding regions. The planar residues are well represented in the active sites, and the geometry of their interactions does not deviate from the general distribution. The geometrical relationship between interacting residues provides valuable insights into the process of protein folding and would be useful for the design of protein molecules and modulation of their binding properties.
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Affiliation(s)
- Pinak Chakrabarti
- Department of Biochemistry and Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India.
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12
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Chandrasekaran A, Ojeda AM, Kolmakova NG, Parsons SM. Mutational and bioinformatics analysis of proline- and glycine-rich motifs in vesicular acetylcholine transporter. J Neurochem 2006; 98:1551-9. [PMID: 16923166 DOI: 10.1111/j.1471-4159.2006.03975.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The vesicular acetylcholine transporter (VAChT) contains six conserved sequence motifs that are rich in proline and glycine. Because these residues can have special roles in the conformation of polypeptide backbone, the motifs might have special roles in conformational changes during transport. Using published bioinformatics insights, the amino acid sequences of the 12 putative, helical, transmembrane segments of wild-type and mutant VAChTs were analyzed for propensity to form non-alpha-helical conformations and molecular notches. Many instances were found. In particular, high propensity for kinks and notches are robustly predicted for motifs D2, C and C'. Mutations in these motifs either increase or decrease Vmax for transport, but they rarely affect the equilibrium dissociation constants for ACh and the allosteric inhibitor, vesamicol. The near absence of equilibrium effects implies that the mutations do not alter the backbone conformation. In contrast, the Vmax effects demonstrate that the mutations alter the difficulty of a major conformational change in transport. Interestingly, mutation of an alanine to a glycine residue in motif C significantly increases the rates for reorientation across the membrane. These latter rates are deduced from the kinetics model of the transport cycle. This mutation is also predicted to produce a more flexible kink and tighter tandem notches than are present in wild-type. For the full set of mutations, faster reorientation rates correlate with greater predicted propensity for kinks and notches. The results of the study argue that conserved motifs mediate conformational changes in the VAChT backbone during transport.
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Affiliation(s)
- Ananda Chandrasekaran
- Department of Chemistry and Biochemistry and Neuroscience Research Institute, University of California, Santa Barbara, California 93106-9510, USA
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13
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Hildebrand PW, Lorenzen S, Goede A, Preissner R. Analysis and prediction of helix–helix interactions in membrane channels and transporters. Proteins 2006; 64:253-62. [PMID: 16555307 DOI: 10.1002/prot.20959] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Membrane proteins span a large variety of different functions such as cell-surface receptors, redox proteins, ion channels, and transporters. Proteins with functional pores show different characteristics of helix-helix packing as other helical membrane proteins. We found that the helix-helix contacts of 13 nonhomologous high-resolution structures of membrane channels and transporters are mainly accomplished by weakly polar amino acids (G > S > T > F) that preferably create contacts every fourth residue, typical for right-handed helix crossings. There is a strong correlation between the now available biological hydrophobicity scale and the propensities of the weakly polar and hydrophobic residues to be buried at helix-helix interfaces or to be exposed to the lipids in membrane channels and transporters. The polar residues, however, make no major contribution towards the packing of their transmembrane helices, and are therefore subsumed to be primarily exposed to the polar milieu during the folding process. The contact formation of membrane channels and transporters is therefore ruled by the solubility of the residues, which we suppose to be the driving force for the assembly of their transmembrane helices. By contrast, in 14 nonhomologous high-resolution structures of other membrane protein coils, also large and polar amino acids (D > S > M > Q) create characteristic contacts every 3.5th residues, which is a signature for left-handed helix crossings. Accordingly, it seems that dependent on the function, different concepts of folding and stabilization are realized for helical membrane proteins. Using a sequence-based matrix prediction method these differences are exploited to improve the prediction of buried and exposed residues of transmembrane helices significantly. When the sequence motifs typical for membrane channels and transporters were applied for the prediction of helix-helix contacts the quality of prediction rises by 16% to an average value of 76%, compared to the same approach when only single amino acid positions are taken into account.
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14
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Ha JH, Kim YS, Hochstrasser RM. Vibrational dynamics of N–H, C–D, and CO modes in formamide. J Chem Phys 2006; 124:64508. [PMID: 16483221 DOI: 10.1063/1.2162165] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
By means of heterodyned two-dimensional IR photon echo experiments on liquid formamide and isotopomers the vibrational frequency dynamics of the N-H stretch mode, the C-D mode, and the C=O mode were obtained. In each case the vibrational frequency correlation function is fitted to three exponentials representing ultrafast (few femtoseconds), intermediate (hundreds of femtoseconds), and slow (many picoseconds) correlation times. In the case of N-H there is a significant underdamped contribution to the correlation decay that was not seen in previous experiments and is attributed to hydrogen-bond librational modes. This underdamped motion is not seen in the C-D or C=O correlation functions. The motions probed by the C-D bond are generally faster than those seen by N-H and C=O, indicating that the environment of C-D interchanges more rapidly, consistent with a weaker C-D...O=C bond. The correlation decays of N-H and C=O are similar, consistent with both being involved in strong H bonding.
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Affiliation(s)
- Jeong-Hyon Ha
- Department of Chemistry, University of Pennsylvania, Philadelphia, 19104, USA
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15
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Thakur AK, Kishore R. Characterization of β-turn and Asx-turns mimicry in a model peptide: Stabilization via CH · · · O interaction. Biopolymers 2006; 81:440-9. [PMID: 16411188 DOI: 10.1002/bip.20441] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The chemical synthesis and single-crystal X-ray diffraction analysis of a model peptide, Boc-Thr-Thr-NH2 (1) comprised of proteinogenic residues bearing an amphiphilic Cbeta -stereogenic center, has been described. Interestingly, the analysis of its molecular structure revealed the existence of a distinct conformation that mimics a typical beta-turn and Asx-turns, i.e., the two Thr residues occupy the left- and right-corner positions. The main-chain torsion angles of the N- and C-terminal residues i.e., semiextended: phi = -68.9 degrees , psi = 128.6 degrees ; semifolded: phi = -138.1 degrees , psi = 2.5 degrees conformations, respectively, in conjunction with a gauche- disposition of the obligatory C-terminus Thr CgammaH3 group, characterize the occurrence of the newly described beta-turn- and Asx-turns-like topology. The preferred molecular structure is suggested to be stabilized by an effective nonconventional main-chain to side-chain Ci=O . . . H--Cgamma(i+2)-type intraturn hydrogen bond. Noteworthy, the observed topology of the resulting 10-membered hydrogen-bonded ring is essentially similar to the one perceived for a classical beta-turn and the Asx-turns, stabilized by a conventional intraturn hydrogen bond. Considering the signs as well as magnitudes of the backbone torsion angles and the orientation of the central peptide bond, the overall mimicked topology resembles the type II beta-turn or type II Asx-turns. An analysis of Xaa-Thr sequences in high-resolution X-ray elucidated protein structures revealed the novel topology prevalence in functional proteins (unpublished). In view of indubitable structural as well as functional importance of nonconventional interactions in bioorganic and biomacromolecules, we intend to highlight the participation of Thr CgammaH in the creation of a short-range C=O . . . H--Cgamma -type interaction in peptides and proteins.
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Affiliation(s)
- A K Thakur
- Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
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16
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Melkozernov AN, Barber J, Blankenship RE. Light Harvesting in Photosystem I Supercomplexes,. Biochemistry 2005; 45:331-45. [PMID: 16401064 DOI: 10.1021/bi051932o] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In photosynthetic membranes of cyanobacteria, algae, and higher plants, photosystem I (PSI) mediates light-driven transmembrane electron transfer from plastocyanin or cytochrome c6 to the ferredoxin-NADP complex. The oxidoreductase function of PSI is sensitized by a reversible photooxidation of primary electron donor P700, which launches a multistep electron transfer via a series of redox cofactors of the reaction center (RC). The excitation energy for the functioning of the primary electron donor in the RC is delivered via the chlorophyll core antenna in the complex with peripheral light-harvesting antennas. Supermolecular complexes of the PSI acquire remarkably different structural forms of the peripheral light-harvesting antenna complexes, including distinct pigment types and organizational principles. The PSI core antenna, being the main functional unit of the supercomplexes, provides an increased functional connectivity in the chlorophyll antenna network due to dense pigment packing resulting in a fast spread of the excitation among the neighbors. Functional connectivity within the network as well as the spectral overlap of antenna pigments allows equilibration of the excitation energy in the depth of the whole membrane within picoseconds and loss-free delivery of the excitation to primary donor P700 within 20-40 ps. Low-light-adapted cyanobacteria under iron-deficiency conditions extend this capacity via assembly of efficiently energy coupled rings of CP43-like complexes around the PSI trimers. In green algae and higher plants, less efficient energy coupling in the eukaryotic PSI-LHCI supercomplexes is probably a result of the structural adaptation of the Chl a/b binding LHCI peripheral antenna that not only extends the absorption cross section of the PSI core but participates in regulation of excitation flows between the two photosystems as well as in photoprotection.
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Affiliation(s)
- Alexander N Melkozernov
- Department of Chemistry and Biochemistry and Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA.
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Yates JR, Pham TN, Pickard CJ, Mauri F, Amado AM, Gil AM, Brown SP. An Investigation of Weak CH···O Hydrogen Bonds in Maltose Anomers by a Combination of Calculation and Experimental Solid-State NMR Spectroscopy. J Am Chem Soc 2005; 127:10216-20. [PMID: 16028932 DOI: 10.1021/ja051019a] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two-dimensional (1)H-(13)C MAS-J-HMQC solid-state NMR spectra of the two anomeric forms of maltose at natural abundance are presented. The experimental (1)H chemical shifts of the CH and CH(2) protons are assigned using first-principles chemical shift calculations that employ a plane-wave pseudopotential approach. Further calculations show that the calculated change in the (1)H chemical shift when comparing the full crystal and an isolated molecule is a quantitative measure of intermolecular C-H...O weak hydrogen bonding. Notably, a clear correlation between a large chemical shift change (up to 2 ppm) and both a short H...O distance (<2.7 A) and a CHO bond angle greater than 130 degrees is observed, thus showing that directionality is important in C-H...O hydrogen bonding.
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Affiliation(s)
- Jonathan R Yates
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, UK
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18
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Guo H, Beahm RF, Guo H. Stabilization and Destabilization of the Cδ−H···OC Hydrogen Bonds Involving Proline Residues in Helices. J Phys Chem B 2004. [DOI: 10.1021/jp0480192] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Robert F. Beahm
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996
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19
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Senes A, Engel DE, DeGrado WF. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol 2004; 14:465-79. [PMID: 15313242 DOI: 10.1016/j.sbi.2004.07.007] [Citation(s) in RCA: 350] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Helical integral membrane proteins share several structural determinants that are widely conserved across their universe. The discovery of common motifs has furthered our understanding of the features that are important to stability in the membrane environment, while simultaneously providing clues about proteins that lack high-resolution structures. Motif analysis also helps to target mutagenesis studies, and other experimental and computational work. Three types of transmembrane motifs have recently seen interesting developments: the GxxxG motif and its like; polar and hydrogen bonding motifs; and proline motifs.
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Affiliation(s)
- Alessandro Senes
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
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20
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Manikandan K, Ramakumar S. The occurrence of CH…O hydrogen bonds in α-helices and helix termini in globular proteins. Proteins 2004; 56:768-81. [PMID: 15281129 DOI: 10.1002/prot.20152] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A comprehensive database analysis of C--H...O hydrogen bonds in 3124 alpha-helices and their corresponding helix termini has been carried out from a nonredundant data set of high-resolution globular protein structures resolved at better than 2.0 A in order to investigate their role in the helix, the important protein secondary structural element. The possible occurrence of 5 --> 1 C--H...O hydrogen bond between the ith residue CH group and (i - 4)th residue C==O with C...O < or = 3.8 A is studied, considering as potential donors the main-chain Calpha and the side-chain carbon atoms Cbeta, Cgamma, Cdelta and Cepsilon. Similar analysis has been carried out for 4 --> 1 C--H...O hydrogen bonds, since the C--H...O hydrogen bonds found in helices are predominantly of type 5 --> 1 or 4 --> 1. A total of 17,367 (9310 of type 5 --> 1 and 8057 of type 4 --> 1) C--H...O hydrogen bonds are found to satisfy the selected criteria. The average stereochemical parameters for the data set suggest that the observed C--H...O hydrogen bonds are attractive interactions. Our analysis reveals that the Cgamma and Cbeta hydrogen atom(s) are frequently involved in such hydrogen bonds. A marked preference is noticed for aliphatic beta-branched residue Ile to participate in 5 --> 1 C--H...O hydrogen bonds involving methylene Cgamma 1 atom as donor in alpha-helices. This may be an enthalpic compensation for the greater loss of side-chain conformational entropy for beta-branched amino acids due to the constraint on side-chain torsion angle, namely, chi1, when they occur in helices. The preference of amino acids for 4 --> 1 C--H...O hydrogen bonds is found to be more for Asp, Cys, and for aromatic residues Trp, Phe, and His. Interestingly, overall propensity for C--H...O hydrogen bonds shows that a majority of the helix favoring residues such as Met, Glu, Arg, Lys, Leu, and Gln, which also have large side-chains, prefer to be involved in such types of weak attractive interactions in helices. The amino acid side-chains that participate in C--H...O interactions are found to shield the acceptor carbonyl oxygen atom from the solvent. In addition, C--H...O hydrogen bonds are present along with helix stabilizing salt bridges. A novel helix terminating interaction motif, X-Gly with Gly at C(cap) position having 5 --> 1 Calpha--H...O, and a chain reversal structural motif having 1 --> 5 Calpha-H...O have been identified and discussed. Our analysis highlights that a multitude of local C--H...O hydrogen bonds formed by a variety of amino acid side-chains and Calpha hydrogen atoms occur in helices and more so at the helix termini. It may be surmised that the main-chain Calpha and the side-chain CH that participate in C--H...O hydrogen bonds collectively augment the cohesive energy and thereby contribute together with the classical N--H...O hydrogen bonds and other interactions to the overall stability of helix and therefore of proteins.
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Affiliation(s)
- K Manikandan
- Department of Physics, Indian Institute of Science, Bangalore, India
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21
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Yohannan S, Faham S, Yang D, Grosfeld D, Chamberlain AK, Bowie JU. A Cα−H···O Hydrogen Bond in a Membrane Protein Is Not Stabilizing. J Am Chem Soc 2004; 126:2284-5. [PMID: 14982414 DOI: 10.1021/ja0317574] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonds involving a carbon donor are very common in protein structures, and energy calculations suggest that Calpha-H...O hydrogen bonds could be about one-half the strength of traditional hydrogen bonds. It has therefore been proposed that these nontraditional hydrogen bonds could be a significant factor in stabilizing proteins, particularly membrane proteins as there is a low dielectric and no competition from water in the bilayer core. Nevertheless, this proposition has never been tested experimentally. Here, we report an experimental test of the significance of Calpha-H...O bonds for protein stability. Thr24 in bacteriorhodopsin, which makes an interhelical Calpha-H...O hydrogen bond to the Calpha of Ala51, was changed to Ala, Val, and Ser, and the thermodynamic stability of the mutants was measured. None of the mutants had significantly reduced stability. In fact, T24A was more stable than the wild-type protein by 0.6 kcal/mol. Crystal structures were determined for each of the mutants, and, while some structural changes were seen for T24S and T24V, T24A showed essentially no apparent structural alteration that could account for the increased stability. Thus, Thr24 appears to destabilize the protein rather than stabilize. Our results suggest that Calpha-H...O bonds are not a major contributor to protein stability.
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Affiliation(s)
- Sarah Yohannan
- Department of Chemistry and Biochemistry, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, 655 Boyer Hall, University of California, Los Angeles, Los Angeles, California 90095-1570, USA
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22
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Curran AR, Engelman DM. Sequence motifs, polar interactions and conformational changes in helical membrane proteins. Curr Opin Struct Biol 2003; 13:412-7. [PMID: 12948770 DOI: 10.1016/s0959-440x(03)00102-7] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The alpha helices of transmembrane proteins interact to form higher order structures. These interactions are frequently mediated by packing motifs (such as GxxxG) and polar residues. Recent structural data have revealed that small sidechains are able to both stabilize helical membrane proteins and allow conformational changes in the structure. The strong interactions involving polar sidechains often contribute to protein misfolding or malfunction.
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Affiliation(s)
- A Rachael Curran
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520-8114, USA
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