1
|
Modrušan M, Glazer L, Otmačić L, Crnolatac I, Cindro N, Vidović N, Piantanida I, Speranza G, Horvat G, Tomišić V. Anion-Binding Properties of Short Linear Homopeptides. Int J Mol Sci 2024; 25:5235. [PMID: 38791275 PMCID: PMC11121566 DOI: 10.3390/ijms25105235] [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: 04/23/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
A comprehensive thermodynamic and structural study of the complexation affinities of tetra (L1), penta (L2), and hexaphenylalanine (L3) linear peptides towards several inorganic anions in acetonitrile (MeCN) and N,N-dimethylformamide (DMF) was carried out. The influence of the chain length on the complexation thermodynamics and structural changes upon anion binding are particularly addressed here. The complexation processes were characterized by means of spectrofluorimetric, 1H NMR, microcalorimetric, and circular dichroism spectroscopy titrations. The results indicate that all three peptides formed complexes of 1:1 stoichiometry with chloride, bromide, hydrogen sulfate, dihydrogen phosphate (DHP), and nitrate anions in acetonitrile and DMF. In the case of hydrogen sulfate and DHP, anion complexes of higher stoichiometries were observed as well, namely those with 1:2 and 2:1 (peptide:anion) complexes. Anion-induced peptide backbone structural changes were studied by molecular dynamic simulations. The anions interacted with backbone amide protons and one of the N-terminal amine protons through hydrogen bonding. Due to the anion binding, the main chain of the studied peptides changed its conformation from elongated to quasi-cyclic in all 1:1 complexes. The accomplishment of such a conformation is especially important for cyclopeptide synthesis in the head-to-tail macrocyclization step, since it is most suitable for ring closure. In addition, the studied peptides can act as versatile ionophores, facilitating transmembrane anion transport.
Collapse
Affiliation(s)
- Matija Modrušan
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Lucija Glazer
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Lucija Otmačić
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Ivo Crnolatac
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.C.); (I.P.)
| | - Nikola Cindro
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Nikolina Vidović
- Faculty of Biotechnology and Drug Development, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka, Croatia;
| | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.C.); (I.P.)
| | - Giovanna Speranza
- Department of Chemistry, University of Milan, Via Golgi 19, 20122 Milan, Italy;
| | - Gordan Horvat
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Vladislav Tomišić
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| |
Collapse
|
2
|
Harrison SA, Naretto A, Balakrishnan S, Perera YR, Chazin WJ. Comparative analysis of the physical properties of murine and human S100A7: Insight into why zinc piracy is mediated by human but not murine S100A7. J Biol Chem 2023; 299:105292. [PMID: 37769710 PMCID: PMC10598741 DOI: 10.1016/j.jbc.2023.105292] [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: 06/01/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023] Open
Abstract
S100 proteins are a subfamily of EF-hand calcium-binding proteins found primarily in vertebrate animals. They are distinguished by binding of transition metals and functioning in both the intracellular and extracellular milieu. S100A7 functions in the protection of the skin and mucous membranes and is a biomarker in inflammatory skin disease. A recent study of Neisseria gonorrhoeae infection revealed that human but not murine S100A7 could be used to evade host nutritional immunity. To understand the molecular basis for this difference, we carried out a comparative analysis of the physical and structural properties of human and murine S100A7. The X-ray crystal structure of Ca2+-loaded mouse S100A7 (mS100A7) was determined to 1.69 Å resolution, and Ca2+-induced conformational changes were assessed by NMR. Unlike human S100A7 (hS100A7), which exhibits conformational changes in response to binding of Ca2+, no significant changes in mS100A7 were detected. Dynamic light scattering, circular dichroism, and a competition chelator assay were used to compare the Zn2+ affinity and the effects of ion binding on mS100A7 versus hS100A7. Alignment of their sequences revealed a substantial difference in the C-terminal region, which is an important mediator of protein-protein interactions, suggesting a rationale for the specificity of N. gonorrhoeae for hS100A7. These data, along with more detailed analysis of S100A7 sequence conservation across different species, support the proposal that, although hS100A7 is highly conserved in many mammals, the murine protein is a distinct ortholog. Our results highlight the potential limitations of using mouse models for studying bacterial infections in humans.
Collapse
Affiliation(s)
- Simone A Harrison
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Anais Naretto
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Swati Balakrishnan
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Yasiru R Perera
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.
| |
Collapse
|
3
|
Leader DP, Milner-White EJ. The conserved crown bridge loop at the catalytic centre of enzymes of the haloacid dehalogenase superfamily. Curr Res Struct Biol 2023; 6:100105. [PMID: 37786806 PMCID: PMC10541634 DOI: 10.1016/j.crstbi.2023.100105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 10/04/2023] Open
Abstract
The crown bridge loop is hexapeptide motif in which the backbone carbonyl group at position 1 is hydrogen bonded to the backbone imino groups of positions 4 and 6. Residues at positions 1 and 4-6 are held in a tight substructure, but different orientations of the plane of the peptide bond between positions 2 and 3 result in two conformers: the 2,3-αRαR crown bridge loop - found in approximately 7% of proteins - and the 2,3-βRαL crown bridge loop, found in approximately 1-2% of proteins. We constructed a relational database in which we identified 60 instances of the 2,3-βRαL conformer, and find that about half occur in enzymes of the haloacid dehalogenase (HAD) superfamily, where they are located next to the catalytic aspartate residue. Analysis of additional enzymes of the HAD superfamily in the extensive SCOPe dataset showed this crown bridge loop to be a conserved feature. Examination of available structures showed that the 2,3-βRαL conformation - but not the 2,3-αRαR conformation - allows the backbone carbonyl group at position 2 to interact with the essential Mg2+ ion. The possibility of interconversion between the 2,3-βRαL and 2,3-αRαR conformations during catalysis is discussed.
Collapse
Affiliation(s)
- David P. Leader
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | | |
Collapse
|
4
|
Mineev KS, Chernykh MA, Motov VV, Prudnikova DA, Pavlenko DM, Kuzmenkov AI, Peigneur S, Tytgat J, Vassilevski AA. A scorpion toxin affecting sodium channels shows double cis-trans isomerism. FEBS Lett 2023; 597:2358-2368. [PMID: 37501371 DOI: 10.1002/1873-3468.14705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Scorpion α-toxins (α-NaTx) inhibiting the inactivation of voltage-gated sodium channels (Nav ) are a well-studied family of small proteins. We previously showed that the structure of α-NaTx specificity module responsible for selective Nav binding is governed by an interplay between the nest and niche protein motifs. Here, we report the solution structure of the toxin Lqq4 from the venom of the scorpion Leiurus quinquestriatus. Unexpectedly, we find that this toxin presents an ensemble of long-lived structurally distinct states. We unequivocally assign these states to the alternative configurations (cis-trans isomers) of two peptide bonds: V56-P57 and C17-G18; neither of the cis isomers has been described in α-NaTx so far. We argue that the native conformational space of α-NaTx is wider than assumed previously.
Collapse
Affiliation(s)
- Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail A Chernykh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladislav V Motov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Daria A Prudnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daniil M Pavlenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey I Kuzmenkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Jan Tytgat
- Toxicology and Pharmacology, KU Leuven, Belgium
| | - Alexander A Vassilevski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| |
Collapse
|
5
|
Sahu S, Banerjee R, Pal D. Intrinsic proclivity of left-handed conformation in large Nest motif peptides inferred from molecular dynamics. J Biomol Struct Dyn 2023:1-10. [PMID: 37464873 DOI: 10.1080/07391102.2023.2236710] [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: 04/26/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
The 'Nest' motif plays a functional role in protein owing to its ligand binding potential aided by geometric concavity. The presence of less favored left-handed conformation (L-state) in its structure makes this concavity possible and in shaping the native chemical environment amenable to stable binding interactions. To understand the persistent appearance of L-state torsion in the Nest motif, we analyzed 0.5μs Molecular Dynamics (MD) simulation trajectories of 35 six-residue peptides (out of a total of 50 large Nest sequences of ≥6 residues) identified in our previous study. Analysis of the MD trajectories of the individual peptides reveals initial L-state in 60% of the peptides persists for >40% of the trajectory. Further, Nests with different sequences appear to adopt a specific conformational state driven by the neighboring L-state residues. The sequences also possess short secondary structures and amino acid repeats, suggesting evolutionary conservation and the specific role of amino acids in locally predisposing the torsion angle to the L-state. These findings help us to understand how L-state conformation is an essential prerequisite in stabilizing the Nest motif and shed light on the sequence-structure-function paradigm in the rational design of peptides and peptidomimetics for therapeutics.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Subhankar Sahu
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Raja Banerjee
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| |
Collapse
|
6
|
Norseeda K, Bin Aziz Pavel F, Rutherford JT, Meer HN, Dureja C, Hurdle JG, Hevener KE, Sun D. Synthesis and evaluation of phenylimidazole FabK inhibitors as new Anti-C. Difficile agents. Bioorg Med Chem 2023; 88-89:117330. [PMID: 37224699 PMCID: PMC10834300 DOI: 10.1016/j.bmc.2023.117330] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023]
Abstract
Previously, 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(5-(pyridin-2-ylthio)thiazol-2-yl)urea bearing a p-bromine substitution was shown to possess selective inhibitory activity against the Clostridioides difficile enoyl-acyl carrier protein (ACP) reductase II enzyme, FabK. Inhibition of CdFabK by this compound translated to promising antibacterial activity in the low micromolar range. In these studies, we sought to expand our knowledge of the SAR of the phenylimidazole CdFabK inhibitor series while improving the potency of the compounds. Three main series of compounds were synthesized and evaluated based on: 1) pyridine head group modifications including the replacement with a benzothiazole moiety, 2) linker explorations, and 3) phenylimidazole tail group modifications. Overall, improvement in the CdFabK inhibition was achieved, while maintaining the whole cell antibacterial activity. Specifically, compounds 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(5-((3-(trifluoromethyl)pyridin-2-yl)thio)thiazol-2-yl)urea, 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(6-(trifluoromethyl)benzo[d]thiazol-2-yl)urea, and 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(6-chlorobenzo[d]thiazol-2-yl)urea showed CdFabK inhibition (IC50 = 0.10 to 0.24 μM), a 5 to 10-fold improvement in biochemical activity relative to 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(5-(pyridin-2-ylthio)thiazol-2-yl)urea, with anti-C. difficile activity ranging from 1.56 to 6.25 μg/mL. Detailed analysis of the expanded SAR, supported by computational analysis, is presented.
Collapse
Affiliation(s)
- Krissada Norseeda
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI 96720, United States
| | - Fahad Bin Aziz Pavel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Jacob T Rutherford
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
| | - Humna N Meer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, United States.
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI 96720, United States.
| |
Collapse
|
7
|
Conserved Structure and Evolution of DPF Domain of PHF10-The Specific Subunit of PBAF Chromatin Remodeling Complex. Int J Mol Sci 2021; 22:ijms222011134. [PMID: 34681795 PMCID: PMC8538644 DOI: 10.3390/ijms222011134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1–3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1–3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation.
Collapse
|
8
|
Pal D, Sahu S, Banerjee R. New facets of larger Nest motifs in proteins. Proteins 2020; 88:1413-1422. [PMID: 32519388 DOI: 10.1002/prot.25961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/06/2020] [Indexed: 11/07/2022]
Abstract
The Nest is a concave-shaped structural motif in proteins formed by consecutive enantiomeric left-handed (L) and right-handed (R) helical conformation of the backbone. This important motif subsumes many turn and helix capping structures and binds electron-rich ligands. Simple Nests are either RL or LR. Larger Nests (>2 residues long) may be RLR, LRL, RLRL, and so forth, being considered as composed of overlapping simple Nests. The larger Nests remain under-explored despite their widely known contributions to protein function. In our study, we address whether the recurrence of enantiomeric geometry in the larger Nests constrains the peptide backbone such that distinct compositional and conformational preferences are seen compared to simple Nests. Our analysis reveals the critical role of the L helical torsion angle in the formation of larger Nests. This can be observed through the higher propensity of residue or secondary structure combinations in LR and LRL backbone conformation in comparison to RL or RLR, although LR/LRL is considerably lower by occurrence. We also find that the most abundant doublets and triplets in Nests have a propensity for particular secondary structures, suggesting a strong sequence-structure relationship in the larger Nest. Overall, our analysis corroborates distinct features of simple and the larger Nests. Such insights would be helpful towards in-vitro design of peptides and peptidomimetic studies.
Collapse
Affiliation(s)
- Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Subhankar Sahu
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Raja Banerjee
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| |
Collapse
|
9
|
Denesyuk AI, Permyakov SE, Johnson MS, Denessiouk K, Permyakov EA. System Approach for Building of Calcium-Binding Sites in Proteins. Biomolecules 2020; 10:biom10040588. [PMID: 32290360 PMCID: PMC7226230 DOI: 10.3390/biom10040588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022] Open
Abstract
We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n−2), Clampn,(n−1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). In these units, the backbone oxygen atom of a residue in position “n” of an amino acid sequence and side-chain oxygen atom of a residue in position “n + i” (i = −2 to +2) directly interact with a metal cation. An analysis of the known “Ca2+-bound niches” in proteins has shown that a system approach based on the simultaneous use of the Clamp units and earlier proposed One-Residue (OR)/Three-Residue (TR) units significantly improves the results of constructing metal cation-binding sites in proteins.
Collapse
Affiliation(s)
- Alexander I. Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
- Correspondence: ; Tel.: +358-2-215-4006
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku 20520, Finland
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
| |
Collapse
|
10
|
An Interfacial Sodium Ion is an Essential Structural Feature of Fluc Family Fluoride Channels. J Mol Biol 2020; 432:1098-1108. [PMID: 31945374 DOI: 10.1016/j.jmb.2020.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/17/2022]
Abstract
Fluc family fluoride channels are assembled as primitive antiparallel homodimers. Crystallographic studies revealed a cation bound at the center of the protein, where it is coordinated at the dimer interface by main chain carbonyl oxygen atoms from the midmembrane breaks in two corresponding transmembrane helices. Here, we show that this cation is a stably bound sodium ion, and although it is not a transported substrate, its presence is required for the channel to adopt an open, fluoride-conducting conformation. The interfacial site is selective for sodium over other cations, except for Li+, which competes with Na+ for binding, but does not support channel activity. The strictly structural role fulfilled by this sodium provides new context to understand the structures, mechanisms, and evolutionary origins of widespread Na+-coupled transporters.
Collapse
|
11
|
Shalaeva DN, Cherepanov DA, Galperin MY, Golovin AV, Mulkidjanian AY. Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism. eLife 2018; 7:e37373. [PMID: 30526846 PMCID: PMC6310460 DOI: 10.7554/elife.37373] [Citation(s) in RCA: 32] [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: 04/09/2018] [Accepted: 11/26/2018] [Indexed: 01/01/2023] Open
Abstract
The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine 'finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases.
Collapse
Affiliation(s)
- Daria N Shalaeva
- School of PhysicsUniversity of OsnabrückOsnabrückGermany
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Dmitry A Cherepanov
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- Semenov Institute of Chemical PhysicsRussian Academy of SciencesMoscowRussia
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Andrey V Golovin
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Armen Y Mulkidjanian
- School of PhysicsUniversity of OsnabrückOsnabrückGermany
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| |
Collapse
|
12
|
Denesyuk AI, Permyakov SE, Johnson MS, Permyakov EA, Denessiouk K. Building kit for metal cation binding sites in proteins. Biochem Biophys Res Commun 2017; 494:311-317. [PMID: 29017922 DOI: 10.1016/j.bbrc.2017.10.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/06/2017] [Indexed: 11/17/2022]
Abstract
Starting with conformations of calcium-binding sites in parvalbumin and integrin (representative structures of EF-hand and calcium blade zones, respectively) we introduce four new different local Ca2+-recognition units in proteins: a one-residue unit type I (ORI); a three-residue unit type I (TRI); a one-residue unit type II (ORII) and a three-residue unit type II (TRII). Based on the amount and nature of variable atoms, the type I and II units theoretically can have four and twelve variants, respectively. Analysis of known "Ca2+-bound functional niches" in proteins revealed presence of almost all possible variants of Ca2+-recognition units in actual structures. Parvalbumin, integrin alpha-IIb and sixteen other proteins with different Ca2+-bound functional niches contain various consecutively joined combinations of OR(I/II) and TR(I/II) units. Such a OR(I/II)+TR(I/II) joint unit forms a tripeptide, which uses three main-chain atoms for metal binding: nitrogenn (Donor), oxygenn (Acceptor) and nitrogenn+2 (Donor). Thus, taken together, the described ORI, TRI, ORII and TRII units can serve as elementary blocks to construct more complex calcium recognizing substructures in a variety of calcium binding sites of unrelated proteins.
Collapse
Affiliation(s)
- Alexander I Denesyuk
- Faculty of Science and Engineering, Åbo Akademi University, Turku 20500, Finland; Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mark S Johnson
- Faculty of Science and Engineering, Åbo Akademi University, Turku 20500, Finland
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia
| | | |
Collapse
|
13
|
Patra P, Ghosh M, Banerjee R, Chakrabarti J. Anion induced conformational preference of C α NN motif residues in functional proteins. Proteins 2017; 85:2179-2190. [PMID: 28905427 DOI: 10.1002/prot.25382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/16/2017] [Accepted: 09/10/2017] [Indexed: 11/12/2022]
Abstract
Among different ligand binding motifs, anion binding Cα NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with Cα NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping Cα NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion.
Collapse
Affiliation(s)
- Piya Patra
- Maulana Abul Kalam Azad University of Technology, West Bengal, (Formerly known as WBUT), BF-142, Sector-I, Saltlake, Kolkata, 700 064, India
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal, (Formerly known as WBUT), BF-142, Sector-I, Saltlake, Kolkata, 700 064, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India.,The Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector-III, Block JD, Salt Lake, Kolkata, 700106, India
| |
Collapse
|
14
|
English CA, Sherman W, Meng W, Gierasch LM. The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains. J Biol Chem 2017; 292:14765-14774. [PMID: 28754691 DOI: 10.1074/jbc.m117.789313] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/19/2017] [Indexed: 12/20/2022] Open
Abstract
Hsp70 molecular chaperones play key roles in cellular protein homeostasis by binding to exposed hydrophobic regions of incompletely folded or aggregated proteins. This crucial Hsp70 function relies on allosteric communication between two well-structured domains: an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD), which are tethered by an interdomain linker. ATP or ADP binding to the NBD alters the substrate-binding affinity of the SBD, triggering functionally essential cycles of substrate binding and release. The interdomain linker is a well-structured participant in the interdomain interface in ATP-bound Hsp70s. By contrast, in the ADP-bound state, exemplified by the Escherichia coli Hsp70 DnaK, the interdomain linker is flexible. Hsp70 interdomain linker sequences are highly conserved; moreover, mutations in this region compromise interdomain allostery. To better understand the role of this region in Hsp70 allostery, we used molecular dynamics simulations to explore the conformational landscape of the interdomain linker in ADP-bound DnaK and supported our simulations by strategic experimental data. We found that while the interdomain linker samples many conformations, it behaves as three relatively ordered segments connected by hinges. As a consequence, the distances and orientations between the NBD and SBD are limited. Additionally, the C-terminal region of the linker forms previously unreported, transient interactions with the SBD, and the predominant linker-docking site is available in only one allosteric state, that with high affinity for substrate. This preferential binding implicates the interdomain linker as a dynamic allosteric switch. The linker-binding site on the SBD is a potential target for small molecule modulators of the Hsp70 allosteric cycle.
Collapse
Affiliation(s)
| | - Woody Sherman
- From the Departments of Biochemistry and Molecular Biology and.,Schrödinger Inc., Cambridge, Massachusetts 02142.,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 and
| | - Wenli Meng
- From the Departments of Biochemistry and Molecular Biology and
| | - Lila M Gierasch
- From the Departments of Biochemistry and Molecular Biology and .,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 and
| |
Collapse
|
15
|
Macdonald CB, Stockbridge RB. A topologically diverse family of fluoride channels. Curr Opin Struct Biol 2017; 45:142-149. [PMID: 28514705 DOI: 10.1016/j.sbi.2017.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 01/13/2023]
Abstract
Dual-topology proteins are likely evolutionary antecedents to a common motif in membrane protein structures, the inverted repeat. A family of fluoride channels, the Flucs, which protect microorganisms, fungi, and plants against cytoplasmic fluoride accumulation, has representatives of all topologies along this evolutionary trajectory, including dual-topology homodimers, antiparallel heterodimers, and, in eukaryotes, fused two-domain proteins with an inverted repeat motif. Recent high-resolution crystal structures of dual-topology homodimers, coupled with extensive functional information about both the homodimers and two-domain Flucs, provide a case study of the co-evolution of fold and function.
Collapse
Affiliation(s)
- Christian B Macdonald
- Program in Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | - Randy B Stockbridge
- Program in Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA.
| |
Collapse
|
16
|
Fung HYJ, Fu SC, Chook YM. Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals. eLife 2017; 6:e23961. [PMID: 28282025 PMCID: PMC5358978 DOI: 10.7554/elife.23961] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/09/2017] [Indexed: 12/14/2022] Open
Abstract
Nuclear export receptor CRM1 binds highly variable nuclear export signals (NESs) in hundreds of different cargoes. Previously we have shown that CRM1 binds NESs in both polypeptide orientations (Fung et al., 2015). Here, we show crystal structures of CRM1 bound to eight additional NESs which reveal diverse conformations that range from loop-like to all-helix, which occupy different extents of the invariant NES-binding groove. Analysis of all NES structures show 5-6 distinct backbone conformations where the only conserved secondary structural element is one turn of helix that binds the central portion of the CRM1 groove. All NESs also participate in main chain hydrogen bonding with human CRM1 Lys568 side chain, which acts as a specificity filter that prevents binding of non-NES peptides. The large conformational range of NES backbones explains the lack of a fixed pattern for its 3-5 hydrophobic anchor residues, which in turn explains the large array of peptide sequences that can function as NESs.
Collapse
MESH Headings
- Active Transport, Cell Nucleus
- Amino Acid Sequence
- Binding Sites
- Cell Nucleus/metabolism
- Cloning, Molecular
- Crystallography, X-Ray
- Gene Expression
- Humans
- Hydrogen Bonding
- Hydrophobic and Hydrophilic Interactions
- Karyopherins/chemistry
- Karyopherins/genetics
- Karyopherins/metabolism
- Models, Molecular
- Nuclear Export Signals
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Thermodynamics
- Exportin 1 Protein
Collapse
Affiliation(s)
- Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Szu-Chin Fu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Jesmita Dhar
- Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, 700 054, India
| | | | | | | | | |
Collapse
|
18
|
Hayward S, Leader DP, Al-Shubailly F, Milner-White EJ. Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides. Proteins 2013; 82:230-9. [DOI: 10.1002/prot.24357] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/10/2013] [Accepted: 06/10/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Steven Hayward
- School of Computing Sciences; University of East Anglia; Norwich NR4 7TJ United Kingdom
| | - David P. Leader
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
| | - Fawzia Al-Shubailly
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
| | - E. James Milner-White
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
| |
Collapse
|
19
|
Egel R. Life's Order, Complexity, Organization, and Its Thermodynamic-Holistic Imperatives. Life (Basel) 2012; 2:323-63. [PMID: 25371269 PMCID: PMC4187152 DOI: 10.3390/life2040323] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/30/2012] [Accepted: 11/05/2012] [Indexed: 12/17/2022] Open
Abstract
In memoriam Jeffrey S. Wicken (1942-2002)-the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken's legacy. (i) Connecting life's origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic 'charging' of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called 'microspheres' is more realistic as a kinetic transition model of primal biogenesis than 'hypercycle replication' theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic 'microspheres'. On the 'continuist vs. miraculist' schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic 'continuist' views and agenda.
Collapse
Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
| |
Collapse
|
20
|
Mielke RE, Robinson KJ, White LM, McGlynn SE, McEachern K, Bhartia R, Kanik I, Russell MJ. Iron-sulfide-bearing chimneys as potential catalytic energy traps at life's emergence. ASTROBIOLOGY 2011; 11:933-950. [PMID: 22111762 DOI: 10.1089/ast.2011.0667] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The concept that life emerged where alkaline hydrogen-bearing submarine hot springs exhaled into the most ancient acidulous ocean was used as a working hypothesis to investigate the nature of precipitate membranes. Alkaline solutions at 25-70°C and pH between 8 and 12, bearing HS(-)±silicate, were injected slowly into visi-jars containing ferrous chloride to partially simulate the early ocean on this or any other wet and icy, geologically active rocky world. Dependent on pH and sulfide content, fine tubular chimneys and geodal bubbles were generated with semipermeable walls 4-100 μm thick that comprised radial platelets of nanometric mackinawite [FeS]±ferrous hydroxide [∼Fe(OH)(2)], accompanied by silica and, at the higher temperature, greigite [Fe(3)S(4)]. Within the chimney walls, these platelets define a myriad of micropores. The interior walls of the chimneys host iron sulfide framboids, while, in cases where the alkaline solution has a pH>11 or relatively low sulfide content, their exteriors exhibit radial flanges with a spacing of ∼4 μm that comprise microdendrites of ferrous hydroxide. We speculate that this pattern results from outward and inward radial flow through the chimney walls. The outer Fe(OH)(2) flanges perhaps precipitate where the highly alkaline flow meets the ambient ferrous iron-bearing fluid, while the intervening troughs signal where the acidulous iron-bearing solutions could gain access to the sulfidic and alkaline interior of the chimneys, thereby leading to the precipitation of the framboids. Addition of soluble pentameric peptides enhances membrane durability and accentuates the crenulations on the chimney exteriors. These dynamic patterns may have implications for acid-base catalysis and the natural proton motive force acting through the matrix of the porous inorganic membrane. Thus, within such membranes, steep redox and pH gradients would bear across the nanometric platelets and separate the two counter-flowing solutions, a condition that may have led to the onset of an autotrophic metabolism through the reduction of carbon dioxide.
Collapse
Affiliation(s)
- Randall E Mielke
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Milner-White EJ, Russell MJ. Functional capabilities of the earliest peptides and the emergence of life. Genes (Basel) 2011; 2:671-88. [PMID: 24710286 PMCID: PMC3927598 DOI: 10.3390/genes2040671] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/14/2011] [Accepted: 09/14/2011] [Indexed: 02/01/2023] Open
Abstract
Considering how biological macromolecules first evolved, probably within a marine environment, it seems likely the very earliest peptides were not encoded by nucleic acids, or at least not via the genetic code as we know it. An objective of the present work is to demonstrate that sequence-independent peptides, or peptides with variable and unreliable lengths and sequences, have the potential to perform a variety of chemically useful functions such as anion and cation binding and membrane and channel formation as well as simple types of catalysis. These functions tend to be performed with the assistance of the main chain CONH atoms rather than the more variable or limited side chain atoms of the peptides presumed to exist then.
Collapse
Affiliation(s)
- E James Milner-White
- College of Medical, Veterinary and Life Sciences, Glasgow University, Glasgow G128QQ, UK.
| | - Michael J Russell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA.
| |
Collapse
|
22
|
Regad L, Martin J, Camproux AC. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs. BMC Bioinformatics 2011; 12:247. [PMID: 21689388 PMCID: PMC3158783 DOI: 10.1186/1471-2105-12-247] [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: 10/07/2010] [Accepted: 06/20/2011] [Indexed: 12/24/2022] Open
Abstract
Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.
Collapse
|
23
|
Kolombet VA, Frolov AI. Na+/K+ selectivity in the formation of ion pairs in aqueous solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793110060011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
The structure of the ends of α-helices in globular proteins: Effect of additional hydrogen bonds and implications for helix formation. Proteins 2011; 79:1010-9. [DOI: 10.1002/prot.22942] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/29/2010] [Accepted: 11/05/2010] [Indexed: 11/07/2022]
|
25
|
Cianci M, Tomaszewski B, Helliwell JR, Halling PJ. Crystallographic Analysis of Counterion Effects on Subtilisin Enzymatic Action in Acetonitrile. J Am Chem Soc 2010; 132:2293-300. [DOI: 10.1021/ja908703c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michele Cianci
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany, WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom, and Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Bartlomiej Tomaszewski
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany, WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom, and Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - John R. Helliwell
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany, WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom, and Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Peter J. Halling
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany, WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom, and Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| |
Collapse
|
26
|
Leader DP, Milner-White EJ. Motivated proteins: a web application for studying small three-dimensional protein motifs. BMC Bioinformatics 2009; 10:60. [PMID: 19210785 PMCID: PMC2651126 DOI: 10.1186/1471-2105-10-60] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 02/11/2009] [Indexed: 11/10/2022] Open
Abstract
Background Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. Description The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. Conclusion Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema.
Collapse
Affiliation(s)
- David P Leader
- Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
| | | |
Collapse
|