1
|
Lameiras P, Nuzillard JM. Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 123:1-50. [PMID: 34078536 DOI: 10.1016/j.pnmrs.2020.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/06/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between 1H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).
Collapse
Affiliation(s)
- Pedro Lameiras
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
| |
Collapse
|
2
|
Fenn J, Nepravishta R, Guy CS, Harrison J, Angulo J, Cameron AD, Fullam E. Structural Basis of Glycerophosphodiester Recognition by the Mycobacterium tuberculosis Substrate-Binding Protein UgpB. ACS Chem Biol 2019; 14:1879-1887. [PMID: 31433162 PMCID: PMC6757277 DOI: 10.1021/acschembio.9b00204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/07/2019] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB) and has evolved an incredible ability to survive latently within the human host for decades. The Mtb pathogen encodes for a low number of ATP-binding cassette (ABC) importers for the acquisition of carbohydrates that may reflect the nutrient poor environment within the host macrophages. Mtb UgpB (Rv2833c) is the substrate binding domain of the UgpABCE transporter that recognizes glycerophosphocholine (GPC), indicating that this transporter has a role in recycling glycerophospholipid metabolites. By using a combination of saturation transfer difference (STD) NMR and X-ray crystallography, we report the structural analysis of Mtb UgpB complexed with GPC and have identified that Mtb UgpB not only recognizes GPC but is also promiscuous for a broad range of glycerophosphodiesters. Complementary biochemical analyses and site-directed mutagenesis precisely define the molecular basis and specificity of glycerophosphodiester recognition. Our results provide critical insights into the structural and functional role of the Mtb UgpB transporter and reveal that the specificity of this ABC-transporter is not limited to GPC, therefore optimizing the ability of Mtb to scavenge scarce nutrients and essential glycerophospholipid metabolites via a single transporter during intracellular infection.
Collapse
Affiliation(s)
- Jonathan
S. Fenn
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Ridvan Nepravishta
- School
of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Collette S. Guy
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - James Harrison
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Jesus Angulo
- School
of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Alexander D. Cameron
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Elizabeth Fullam
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| |
Collapse
|
3
|
Babii O, Afonin S, Ishchenko AY, Schober T, Negelia AO, Tolstanova GM, Garmanchuk LV, Ostapchenko LI, Komarov IV, Ulrich AS. Structure–Activity Relationships of Photoswitchable Diarylethene-Based β-Hairpin Peptides as Membranolytic Antimicrobial and Anticancer Agents. J Med Chem 2018; 61:10793-10813. [DOI: 10.1021/acs.jmedchem.8b01428] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Oleg Babii
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Aleksandr Yu. Ishchenko
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Vul. Volodymyrska 60, 01601 Kyiv, Ukraine
- Enamine Ltd., Vul. Chervonotkatska 78, 02066 Kyiv, Ukraine
| | - Tim Schober
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Anatoliy O. Negelia
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Ganna M. Tolstanova
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Liudmyla V. Garmanchuk
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Liudmyla I. Ostapchenko
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Igor V. Komarov
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Vul. Volodymyrska 60, 01601 Kyiv, Ukraine
- Enamine Ltd., Vul. Chervonotkatska 78, 02066 Kyiv, Ukraine
- Lumobiotics GmbH, Auerstraße 2, 76227 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| |
Collapse
|
4
|
Antimicrobial peptides produced by Brevibacillus spp.: structure, classification and bioactivity: a mini review. World J Microbiol Biotechnol 2018; 34:57. [DOI: 10.1007/s11274-018-2437-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
|
5
|
Pereverzev AY, Boyarkin OV. Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A. Phys Chem Chem Phys 2018; 19:3468-3472. [PMID: 28106178 DOI: 10.1039/c6cp07953a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.
Collapse
Affiliation(s)
- A Y Pereverzev
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - O V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| |
Collapse
|
6
|
Guzzi C, Alfarano P, Sutkeviciute I, Sattin S, Ribeiro-Viana R, Fieschi F, Bernardi A, Weiser J, Rojo J, Angulo J, Nieto PM. Detection and quantitative analysis of two independent binding modes of a small ligand responsible for DC-SIGN clustering. Org Biomol Chem 2016; 14:335-44. [DOI: 10.1039/c5ob02025e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Multiple binding modes at the same binding site can explain the higher binding affinity of a pseudotrimannotrioside compared to a pseudomannobioside.
Collapse
Affiliation(s)
- C. Guzzi
- Glycosystems Laboratory. Instituto de Investigaciones Químicas (IIQ)/cicCartuja. CSIC/US
- 41092 Sevilla
- Spain
- Dept. of Biotechnology and Biosciences University of Millano-Bicocca Piazza della Scienza 2 20126
- Milan
| | - P. Alfarano
- Anterio Consult & Research GmbH
- Augustaanlage 23 68165 Mannheim
- Germany
| | - I. Sutkeviciute
- Univ. Grenoble Alpes
- Institut de Biologie Structurale (IBS)
- F-38044 Grenoble
- France
- CNRS
| | - S. Sattin
- Dipartimento di Chimica
- Universita’ degli Studi di Milano
- 20133 Milano
- Italy
| | - R. Ribeiro-Viana
- Glycosystems Laboratory. Instituto de Investigaciones Químicas (IIQ)/cicCartuja. CSIC/US
- 41092 Sevilla
- Spain
| | - F. Fieschi
- Univ. Grenoble Alpes
- Institut de Biologie Structurale (IBS)
- F-38044 Grenoble
- France
- CNRS
| | - A. Bernardi
- Dipartimento di Chimica
- Universita’ degli Studi di Milano
- 20133 Milano
- Italy
| | - J. Weiser
- Anterio Consult & Research GmbH
- Augustaanlage 23 68165 Mannheim
- Germany
| | - J. Rojo
- Glycosystems Laboratory. Instituto de Investigaciones Químicas (IIQ)/cicCartuja. CSIC/US
- 41092 Sevilla
- Spain
| | - J. Angulo
- Glycosystems Laboratory. Instituto de Investigaciones Químicas (IIQ)/cicCartuja. CSIC/US
- 41092 Sevilla
- Spain
- School of Pharmacy
- University of East Anglia
| | - P. M. Nieto
- Glycosystems Laboratory. Instituto de Investigaciones Químicas (IIQ)/cicCartuja. CSIC/US
- 41092 Sevilla
- Spain
| |
Collapse
|
7
|
Kubyshkin V, Afonin S, Kara S, Budisa N, Mykhailiuk PK, Ulrich AS. γ-(S)-Trifluoromethyl proline: evaluation as a structural substitute of proline for solid state (19)F-NMR peptide studies. Org Biomol Chem 2015; 13:3171-3181. [PMID: 25703116 DOI: 10.1039/c5ob00034c] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
γ-(4S)-Trifluoromethyl proline was synthesised according to a modified literature protocol with improved yield on a multigram scale. Conformational properties of the amide bond formed by the amino acid were characterised using N-acetyl methyl ester model. The amide populations (s-trans vs. s-cis) and thermodynamic parameters of the isomerization were found to be similar to the corresponding values for intact proline. Therefore, the γ-trifluoromethyl proline was suggested as a structurally low-disturbing proline substitution in peptides for their structural studies by (19)F-NMR. Indeed, the exchange of native proline for γ-trifluoromethyl proline in the peptide antibiotic gramicidin S was shown to preserve the overall amphipathic peptide structure. The utility of the amino acid as a selective (19)F-NMR label was demonstrated by observing the re-alignment of the labelled gramicidin S in oriented lipid bilayers.
Collapse
Affiliation(s)
- Vladimir Kubyshkin
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany. and Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), KIT, POB 3640, 76021 Karlsruhe, Germany
| | - Sezgin Kara
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Pavel K Mykhailiuk
- Faculty of Chemistry, Taras Shevchenko National University of Kyiv, vul. Volodymyrska 62a, 01601 Kyiv, Ukraine. and Enamine Ltd., vyl. Chervonotkatska 78, 02660 Kyiv, Ukraine
| | - Anne S Ulrich
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany. and Institute of Biological Interfaces (IBG-2), KIT, POB 3640, 76021 Karlsruhe, Germany
| |
Collapse
|
8
|
Fermentation and Cost-Effective 13C/15N Labeling of the Nonribosomal Peptide Gramicidin S for Nuclear Magnetic Resonance Structure Analysis. Appl Environ Microbiol 2015; 81:3593-603. [PMID: 25795666 DOI: 10.1128/aem.00229-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/04/2015] [Indexed: 11/20/2022] Open
Abstract
Gramicidin S (GS) is a nonribosomally synthesized decapeptide from Aneurinibacillus migulanus. Its pronounced antibiotic activity is attributed to amphiphilic structure and enables GS interaction with bacterial membranes. Despite its medical use for over 70 years, the peptide-lipid interactions of GS and its molecular mechanism of action are still not fully understood. Therefore, a comprehensive structural analysis of isotope-labeled GS needs to be performed in its biologically relevant membrane-bound state, using advanced solid-state nuclear magnetic resonance (NMR) spectroscopy. Here, we describe an efficient method for producing the uniformly (13)C/(15)N-labeled peptide in a minimal medium supplemented by selected amino acids. As GS is an intracellular product of A. migulanus, we characterized the producer strain DSM 5759 (rough-convex phenotype) and examined its biosynthetic activity in terms of absolute and biomass-dependent peptide accumulation. We found that the addition of either arginine or ornithine increases the yield only at very high supplementing concentrations (1% and 0.4%, respectively) of these expensive (13)C/(15)N-labeled amino acids. The most cost-effective production of (13)C/(15)N-GS, giving up to 90 mg per gram of dry cell weight, was achieved in a minimal medium containing 1% (13)C-glycerol and 0.5% (15)N-ammonium sulfate, supplemented with only 0.025% of (13)C/(15)N-phenylalanine. The 100% efficiency of labeling is corroborated by mass spectrometry and preliminary solid-state NMR structure analysis of the labeled peptide in the membrane-bound state.
Collapse
|
9
|
3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides. Biophys J 2015; 106:2385-94. [PMID: 24896117 DOI: 10.1016/j.bpj.2014.04.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 11/22/2022] Open
Abstract
The interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shape. Here, we define the hydrophobic moment of a molecule as a vector in three dimensions by evaluating the surface distribution of all hydrophilic and lipophilic regions over any given shape. The electrostatic potential on the molecular surface is calculated based on the atomic point charges. The resulting hydrophobic moment vector is specific for the instantaneous conformation, and it takes into account all structural characteristics of the molecule, e.g., partial unfolding, bending, and side-chain torsion angles. Extended all-atom molecular dynamics simulations are then used to calculate the equilibrium hydrophobic moments for two antimicrobial peptides, gramicidin S and PGLa, under different conditions. We show that their effective hydrophobic moment vectors reflect the distribution of polar and nonpolar patches on the molecular surface and the calculated electrostatic surface potential. A comparison of simulations in solution and in lipid membranes shows how the peptides undergo internal conformational rearrangement upon binding to the bilayer surface. A good correlation with solid-state NMR data indicates that the hydrophobic moment vector can be used to predict the membrane binding geometry of peptides. This method is available as a web application on http://www.ibg.kit.edu/HM/.
Collapse
|
10
|
Babii O, Afonin S, Berditsch M, Reiβer S, Mykhailiuk PK, Kubyshkin VS, Steinbrecher T, Ulrich AS, Komarov IV. Controlling Biological Activity with Light: Diarylethene-Containing Cyclic Peptidomimetics. Angew Chem Int Ed Engl 2014; 53:3392-5. [DOI: 10.1002/anie.201310019] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/13/2014] [Indexed: 11/10/2022]
|
11
|
Babii O, Afonin S, Berditsch M, Reiβer S, Mykhailiuk PK, Kubyshkin VS, Steinbrecher T, Ulrich AS, Komarov IV. Controlling Biological Activity with Light: Diarylethene-Containing Cyclic Peptidomimetics. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
12
|
Antonini LV, Peregrina JR, Angulo J, Medina M, Nieto PM. A STD-NMR study of the interaction of the Anabaena ferredoxin-NADP+ reductase with the coenzyme. Molecules 2014; 19:672-85. [PMID: 24402199 PMCID: PMC6272016 DOI: 10.3390/molecules19010672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/17/2013] [Accepted: 12/18/2013] [Indexed: 11/16/2022] Open
Abstract
Ferredoxin-NADP+ reductase (FNR) catalyzes the electron transfer from ferredoxin to NADP+ via its flavin FAD cofactor. To get further insights in the architecture of the transient complexes produced during the hydride transfer event between the enzyme and the NADP+ coenzyme we have applied NMR spectroscopy using Saturation Transfer Difference (STD) techniques to analyze the interaction between FNRox and the oxidized state of its NADP+ coenzyme. We have found that STD NMR, together with the use of selected mutations on FNR and of the non-FNR reacting coenzyme analogue NAD+, are appropriate tools to provide further information about the the interaction epitope.
Collapse
Affiliation(s)
- Lara V Antonini
- Instituto de Investigaciones Químicas, CSIC, Americo Vespucio, 49, Sevilla 41092, Spain.
| | - José R Peregrina
- Instituto de Investigaciones Químicas, CSIC, Americo Vespucio, 49, Sevilla 41092, Spain.
| | - Jesús Angulo
- Instituto de Investigaciones Químicas, CSIC, Americo Vespucio, 49, Sevilla 41092, Spain.
| | - Milagros Medina
- Instituto de Investigaciones Químicas, CSIC, Americo Vespucio, 49, Sevilla 41092, Spain.
| | - Pedro M Nieto
- Instituto de Investigaciones Químicas, CSIC, Americo Vespucio, 49, Sevilla 41092, Spain.
| |
Collapse
|
13
|
Abstract
The recent introduction of saturation transfer difference (STD) NMR has increased the tools for the study of protein–carbohydrate complexes. This is useful when it is combined with transfer nuclear Overhauser enhancement spectroscopy (NOESY) measurement, or when it is interpreted using the expected calculated values of transference, yielding additional, very valuable information for the study of this type of complex. The objective of this work is to cover the advances of the STD technique as exemplified by the investigations of DC-SIGN (dendritic cell-specific ICAM-3 grabbing non-integrin) recognition by simple carbohydrates or mimics of them, based on structures containing a terminal mannose or fucose. We also will discuss the methods for quantification of the STD values based on the initial growing rates with the saturation time.
Collapse
|
14
|
Thépaut M, Guzzi C, Sutkeviciute I, Sattin S, Ribeiro-Viana R, Varga N, Chabrol E, Rojo J, Bernardi A, Angulo J, Nieto PM, Fieschi F. Structure of a Glycomimetic Ligand in the Carbohydrate Recognition Domain of C-type Lectin DC-SIGN. Structural Requirements for Selectivity and Ligand Design. J Am Chem Soc 2013; 135:2518-29. [DOI: 10.1021/ja3053305] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michel Thépaut
- Institut de Biologie Structurale, Université Grenoble I, 41 rue Jules Horowitz,
Grenoble, F-38027, France
- CNRS, UMR 5075, Grenoble, F-38000, France
- CEA, DSV, Grenoble, F-38000, France
| | - Cinzia Guzzi
- Glycosystems
Laboratory, Instituto
de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Américo Vespucio 49,
41092 Sevilla, Spain
| | - Ieva Sutkeviciute
- Institut de Biologie Structurale, Université Grenoble I, 41 rue Jules Horowitz,
Grenoble, F-38027, France
- CNRS, UMR 5075, Grenoble, F-38000, France
- CEA, DSV, Grenoble, F-38000, France
| | - Sara Sattin
- Dipartimento di Chimica via
Golgi 19, Universita’ di Milano,
20133 Milano, Italy
| | - Renato Ribeiro-Viana
- Glycosystems
Laboratory, Instituto
de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Américo Vespucio 49,
41092 Sevilla, Spain
| | - Norbert Varga
- Dipartimento di Chimica via
Golgi 19, Universita’ di Milano,
20133 Milano, Italy
| | - Eric Chabrol
- Institut de Biologie Structurale, Université Grenoble I, 41 rue Jules Horowitz,
Grenoble, F-38027, France
- CNRS, UMR 5075, Grenoble, F-38000, France
- CEA, DSV, Grenoble, F-38000, France
| | - Javier Rojo
- Glycosystems
Laboratory, Instituto
de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Américo Vespucio 49,
41092 Sevilla, Spain
| | - Anna Bernardi
- Dipartimento di Chimica via
Golgi 19, Universita’ di Milano,
20133 Milano, Italy
| | - Jesus Angulo
- Glycosystems
Laboratory, Instituto
de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Américo Vespucio 49,
41092 Sevilla, Spain
| | - Pedro M. Nieto
- Glycosystems
Laboratory, Instituto
de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Américo Vespucio 49,
41092 Sevilla, Spain
| | - Franck Fieschi
- Institut de Biologie Structurale, Université Grenoble I, 41 rue Jules Horowitz,
Grenoble, F-38027, France
- CNRS, UMR 5075, Grenoble, F-38000, France
- Institut Universitaire de France, 103 boulevard Saint-Michel 75005 Paris, France
| |
Collapse
|
15
|
Nagornova NS, Rizzo TR, Boyarkin OV. Interplay of Intra- and Intermolecular H-Bonding in a Progressively Solvated Macrocyclic Peptide. Science 2012; 336:320-3. [DOI: 10.1126/science.1218709] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
16
|
Joshi K, Semrouni D, Ohanessian G, Clavaguéra C. Structures and IR Spectra of the Gramicidin S Peptide: Pushing the Quest for Low-Energy Conformations. J Phys Chem B 2011; 116:483-90. [DOI: 10.1021/jp207102v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kaustubh Joshi
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - David Semrouni
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Ohanessian
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Carine Clavaguéra
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| |
Collapse
|
17
|
Nagornova NS, Guglielmi M, Doemer M, Tavernelli I, Rothlisberger U, Rizzo TR, Boyarkin OV. Kalte Ionenspektroskopie zur Lösung der Gasphasenstruktur eines Decapeptids. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
18
|
Nagornova NS, Guglielmi M, Doemer M, Tavernelli I, Rothlisberger U, Rizzo TR, Boyarkin OV. Cold-Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide. Angew Chem Int Ed Engl 2011; 50:5383-6. [DOI: 10.1002/anie.201100702] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/07/2011] [Indexed: 11/09/2022]
|
19
|
Guzzi C, Angulo J, Doro F, Reina JJ, Thépaut M, Fieschi F, Bernardi A, Rojo J, Nieto PM. Insights into molecular recognition of LewisX mimics by DC-SIGN using NMR and molecular modelling. Org Biomol Chem 2011; 9:7705-12. [DOI: 10.1039/c1ob05938f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
20
|
Kupser P, Pagel K, Oomens J, Polfer N, Koksch B, Meijer G, von Helden G. Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase. J Am Chem Soc 2010; 132:2085-93. [DOI: 10.1021/ja909842j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Kupser
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Jos Oomens
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Nick Polfer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Beate Koksch
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| |
Collapse
|
21
|
Mogi T, Kita K. Gramicidin S and polymyxins: the revival of cationic cyclic peptide antibiotics. Cell Mol Life Sci 2009; 66:3821-6. [PMID: 19701717 PMCID: PMC11115702 DOI: 10.1007/s00018-009-0129-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 08/10/2009] [Accepted: 08/10/2009] [Indexed: 01/02/2023]
Abstract
Gramicidin S and polymyxins are small cationic cyclic peptides and act as potent antibiotics against Gram-negative and Gram-positive bacteria by perturbing integrity of the bacterial membranes. Screening of a natural antibiotics library with bacterial membrane vesicles identified gramicidin S as an inhibitor of cytochrome bd quinol oxidase and an alternative NADH dehydrogenase (NDH-2) and polymyxin B as an inhibitor of NDH-2 and malate: quinone oxidoreductase. Our studies showed that cationic cyclic peptide antibiotics have novel molecular targets in the membrane and interfere ligand binding on the hydrophobic surface of enzymes. Improvement of the toxicity and optimization of the structures and clinical uses are urgently needed for their effective application in combating drug-resistant bacteria.
Collapse
Affiliation(s)
- Tatsushi Mogi
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| |
Collapse
|
22
|
Bader R. Utilizing the charge field effect on amide (15)N chemical shifts for protein structure validation. J Phys Chem B 2009; 113:347-58. [PMID: 19118488 DOI: 10.1021/jp807362v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Of all the nuclei in proteins, the nuclear magnetic resonance (NMR) chemical shifts of nitrogen are the theoretically least well understood. In this study, quantum chemical methods are used in combination with polarizable-continuum models in order to show that consideration of the effective electric field, including charge screening due to solvation, improves considerably the consistencies of statistical relationships between experimental and computed amide (15)N shifts between various sets of charged and uncharged oligopeptides and small organic molecules. A single conversion scheme between shielding parameters from first principles using density functional theory (DFT) and experimental shifts is derived that holds for all classes of compounds examined here. This relationship is then used to test the accuracy of such (15)N chemical shift predictions in the cyclic decapeptide antibiotic gramicidin S (GS). GS has previously been studied in great detail, both by NMR and X-ray crystallography. It adopts a well-defined backbone conformation, and hence, only a few discrete side chain conformational states need to be considered. Moreover, a charge-relay effect of the two cationic ornithine side chains to the protein backbone has been described earlier by NMR spectroscopy. Here, DFT-derived backbone amide nitrogen chemical shifts were calculated for multiple conformations of GS. Overall, the structural dynamics of GS is revisited in view of chemical shift behavior along with energetic considerations. Together, the study demonstrates proof of concept that (15)N chemical shift information is particularly useful in the analysis and validation of protein conformational states in a charged environment.
Collapse
Affiliation(s)
- Reto Bader
- Department of Physics, Stockholm University, Arrhenius Laboratories, 106 91 Stockholm, Sweden.
| |
Collapse
|
23
|
Gramicidin S identified as a potent inhibitor for cytochrome bd
-type quinol oxidase. FEBS Lett 2008; 582:2299-302. [DOI: 10.1016/j.febslet.2008.05.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 05/21/2008] [Indexed: 01/14/2023]
|
24
|
Solid State NMR Structure Analysis of the Antimicrobial Peptide Gramicidin S in Lipid Membranes: Concentration-Dependent Re-alignment and Self-Assembly as a β-Barrel. Top Curr Chem (Cham) 2008; 273:139-54. [DOI: 10.1007/128_2007_20] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
25
|
Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand–Receptor Complexes. Top Curr Chem (Cham) 2007; 273:15-54. [DOI: 10.1007/128_2007_144] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
26
|
Berditsch M, Afonin S, Ulrich AS. The ability of Aneurinibacillus migulanus (Bacillus brevis) to produce the antibiotic gramicidin S is correlated with phenotype variation. Appl Environ Microbiol 2007; 73:6620-8. [PMID: 17720841 PMCID: PMC2075075 DOI: 10.1128/aem.00881-07] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phenotype instability of bacterial strains can cause significant problems in biotechnological applications, since industrially useful properties may be lost. Here we report such degenerative dissociation for Aneurinibacillus migulanus (formerly known as Bacillus brevis) an established producer of the antimicrobial peptide gramicidin S (GS). Phenotypic variations within and between various strains maintained in different culture collections are demonstrated. The type strain, ATCC 9999, consists of six colony morphology variants, R, RC, RP, RT, SC, and SP, which were isolated and characterized as pure cultures. Correlations between colony morphology, growth, GS production, spore formation, and resistance to their own antimicrobial peptide were established in this study. We found the original R form to be the best producer, followed by RC, RP, and RT, while SC and SP yielded no GS at all. Currently available ATCC 9999(T) contains only 2% of the original R producer and is dominated by the newly described phenotypes RC and RP. No original R form is detected in the nominally equivalent strain DSM 2895(T) (=ATCC 9999(T)), which grows only as SC and SP phenotypes and has thus completely lost its value as a peptide producer. Two other strains from the same collection, DSM 5668 and DSM 5759, contain the unproductive SC variant and the GS-producing RC form, respectively. We describe the growth and maintenance conditions that stabilize certain colony phenotypes and reduce the degree of degenerative dissociation, thus providing a recommendation for how to revert the nonproducing smooth phenotypes to the valuable GS-producing rough ones.
Collapse
Affiliation(s)
- Marina Berditsch
- University of Karlsruhe (TH), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | | | | |
Collapse
|
27
|
Gronwald W, Brunner K, Kirchhöfer R, Trenner J, Neidig KP, Kalbitzer HR. AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein solution structures. JOURNAL OF BIOMOLECULAR NMR 2007; 37:15-30. [PMID: 17136423 DOI: 10.1007/s10858-006-9096-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 09/20/2006] [Indexed: 05/12/2023]
Abstract
We present here the computer program AUREMOL-RFAC-3D that is a generalization of the previously published program RFAC for the fully automated estimation of residual indices (R-factors) from 2D NOESY spectra. It is part of the larger AUREMOL software package (www.auremol.de). RFAC-3D calculates R-factors directly from two-dimensional homonuclear NOESY spectra as well as from three-dimensional (15)N or (13)C edited NOESY-HSQC spectra and thus extends the application range to larger proteins. The fully automated method includes automated peak picking and integration, a Bayesian noise and artifact recognition and the use of the complete relaxation matrix formalism. To enhance the reliability of the calculated R-factors the method is also generalized to calculate combined R-factors from a set of 2D and 3D-spectra. For an optimal combination of the information derived from different sources a plausible formalism had to be derived. In addition, we present a novel direct R-factors based measure that correlates an R-factors as defined in this paper to the root mean square deviation of the actual structure from the optimal structure. The new program has been successfully tested on the histidine containing phosphocarrier protein (HPr) from Staphylococcus carnosus and on the Ras-binding domain (RBD) of the Ral guanine-nucleotide dissociation stimulation factor (RalGDS).
Collapse
Affiliation(s)
- Wolfram Gronwald
- Department of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstr.31, D-93040, Regensburg, Federal Republic of Germany
| | | | | | | | | | | |
Collapse
|
28
|
Jayalakshmi V, Krishna NR. Determination of the Conformation of Trimethoprim in the Binding Pocket of Bovine Dihydrofolate Reductase from a STD-NMR Intensity-Restrained CORCEMA-ST Optimization. J Am Chem Soc 2005; 127:14080-4. [PMID: 16201830 DOI: 10.1021/ja054192f] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) is a pharmacologically important intracellular target enzyme for folate antagonists, including the antibacterial agent trimethoprim (TMP). The structures of DHFR from various sources with and without the bound ligands have been determined by X-ray crystallography and solution NMR spectroscopy. However, there is no crystal or solution NMR structure for the bovine DHFR/TMP complex. Here we report the solution structure of TMP within the binding pocket of bovine DHFR using a novel method developed in our laboratory, viz., STD-NMR intensity-restrained CORCEMA-ST optimization (SICO) utilizing experimental STD data on this complex, and demonstrate that its solution structure is essentially identical to the one in the crystal structure of the homologous chicken liver DHFR/TMP complex. The excellent agreement we obtain between the experimental and predicted STDs also serves as a validation of the CORCEMA-ST methodology.
Collapse
Affiliation(s)
- V Jayalakshmi
- Department of Biochemistry and Molecular Genetics and the NMR Core Facility, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294-2041, USA
| | | |
Collapse
|
29
|
Jayalakshmi V, Biet T, Peters T, Krishna NR. Refinement of the conformation of UDP-galactose bound to galactosyltransferase using the STD NMR intensity-restrained CORCEMA optimization. J Am Chem Soc 2004; 126:8610-1. [PMID: 15250687 DOI: 10.1021/ja048703u] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The STD NMR technique has originally been described as a tool for screening large compound libraries to identify the lead compounds that are specific to target proteins of interest. The application of this technique in the qualitative epitope mapping of ligands weakly binding to proteins, virus capsid shells, and nucleic acids has also been described. Here we describe the application of the STD NMR intensity-restrained CORCEMA optimization (SICO) procedure for refining the bound conformation of UDP-galactose in galactosyltransferase complex using STD NMR intensities recorded at 500 MHz as the experimental constraints. A comparison of the SICO structure for the bound UDP-galactose in solution with that in the crystal structure for this complex shows some differences in ligand torsion angles and V253 side-chain orientation in the protein. This work describes the first application of an STD NMR intensity-restrained CORCEMA optimization procedure for refining the torsion angles of a bound ligand structure. This method is likely to be useful in structure-based drug design programs since most initial lead compounds generally exhibit weak affinity (millimolar to micromolar) to target proteins of pharmaceutical interest, and the bound conformation of these lead compounds in the protein binding pocket can be determined by the CORCEMA-ST refinement.
Collapse
Affiliation(s)
- V Jayalakshmi
- Department of Biochemistry and Molecular Genetics, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294-2041, USA
| | | | | | | |
Collapse
|
30
|
Jayalakshmi V, Rama Krishna N. CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 168:36-45. [PMID: 15082247 DOI: 10.1016/j.jmr.2004.01.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Revised: 01/20/2004] [Indexed: 05/24/2023]
Abstract
We describe an intensity-restrained optimization procedure for refining approximate structures of ligands within the protein binding pockets using STD-NMR intensity data on reversibly forming weak complexes. In this approach, the global minimum for the bound-ligand conformation is obtained by a hybrid structure refinement method involving CORCEMA calculation of intensities and simulated annealing optimization of torsion angles of the bound ligand using STD-NMR intensities as experimental constraints and the NOE R-factor as the pseudo-energy function to be minimized. This method is illustrated using simulated STD data sets for typical carbohydrate and peptide ligands. Our procedure also allows for the optimization of side chain torsion angles of protein residues within the binding pocket. This procedure is useful in refining and improving initial models based on crystallography or computer docking or other algorithms to generate models for the bound ligand (e.g., a lead compound) within the protein binding pocket compatible with solution STD-NMR data. This method may facilitate structure-based drug design efforts.
Collapse
Affiliation(s)
- V Jayalakshmi
- Department of Biochemistry and Molecular Genetics and the NMR Core Facility, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294-2041, USA.
| | | |
Collapse
|
31
|
Lee DL, Hodges RS. Structure-activity relationships of de novo designed cyclic antimicrobial peptides based on gramicidin S. Biopolymers 2003; 71:28-48. [PMID: 12712499 DOI: 10.1002/bip.10374] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The cyclic beta-sheet structure possessed by the 10-residue antibiotic peptide gramicidin S was taken as the structural framework for the de novo design of biologically active peptides with membrane-active properties. We have shown from previous studies that gramicidin S is a broad-spectrum antibiotic effective against Gram-positive bacteria, Gram-negative bacteria, and fungi, but is toxic to human red blood cells. We tested the effect of ring size on antimicrobial activity and hemolytic activity on peptides varying from 4 to 16 residues. Interestingly, we were able to dissociate hemolytic activity and antimicrobial activity by increasing the ring size of the peptide to 14 residues (peptide GS14). Furthermore, we increased specificity for microbial membranes while decreasing toxicity to red blood cells by substituting enantiomers (D-amino acids for L-amino acids and vice versa) into the GS14 sequence. The enantiomeric substitutions all disrupted beta-sheet structure in benign medium and decreased peptide amphipathicity. The least amphipathic peptide, produced by substituting a D-Lys at position 4 of GS14 (peptide GS14K4), also had the highest therapeutic index, i.e., highest degree of specificity for microbial cells over human cells. Solution structures of GS14 analogs solved by NMR spectroscopy showed that the D-amino acid side chain was located on the nonpolar face of GS14K4. Another analog, a beta-sheet peptide with reduced amphipathicity (peptide GS14 K3L4), also had a lysine (lysine 3) on the nonpolar face as determined by the NMR structure. Both GS14K4 and GS14 K3L4 had reduced amphipathicity relative to GS14 and much higher therapeutic indices. Finally, the alteration of the nonpolar face hydrophobicity of GS14K4 analogs provided a range of activities and specificities, where the peptides with the intermediate hydrophobicities among the series had the highest therapeutic indices. The optimal peptide hydrophobicities varied depending on the microorganism being tested, with higher hydrophobicity requirements against Gram-positive bacteria and yeast compared with Gram-negative microorganisms. The net result of these studies suggests that it is possible to rationally design a cyclic membrane-active antimicrobial peptide with high specificity towards prokaryotic (bacterial and fungal) membranes and minimal toxicity to eukaryotic (e.g., mammalian) membranes.
Collapse
Affiliation(s)
- Darin L Lee
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | |
Collapse
|
32
|
Jayalakshmi V, Krishna NR. Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 155:106-118. [PMID: 11945039 DOI: 10.1006/jmre.2001.2499] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A couple of recent applications of intermolecular NOE (INOE) experiments as applied to biomolecular systems involve the (i) saturation transfer difference NMR (STD-NMR) method and (ii) the intermolecular cross-saturation NMR (ICS-NMR) experiment. STD-NMR is a promising tool for rapid screening of a large library of compounds to identify bioactive ligands binding to a target protein. Additionally, it is also useful in mapping the binding epitopes presented by a bioactive ligand to its target protein. In this latter application, the STD-NMR technique is essentially similar to the ICS-NMR experiment, which is used to map protein-protein or protein-nucleic acid contact surfaces in complexes. In this work, we present a complete relaxation and conformational exchange matrix (CORCEMA) theory (H. N. B. Moseley et al., J. Magn. Reson. B 108, 243-261 (1995)) applicable for these two closely related experiments. As in our previous work, we show that when exchange is fast on the relaxation rate scale, a simplified CORCEMA theory can be formulated using a generalized average relaxation rate matrix. Its range of validity is established by comparing its predictions with those of the exact CORCEMA theory which is valid for all exchange rates. Using some ideal model systems we have analyzed the factors that influence the ligand proton intensity changes when the resonances from some protons on the receptor protein are saturated. The results show that the intensity changes in the ligand signals in an intermolecular NOE experiment are very much dependent upon: (1) the saturation time, (2) the location of the saturated receptor protons with respect to the ligand protons, (3) the conformation of the ligand-receptor interface, (4) the rotational correlation times for the molecular species, (5) the kinetics of the reversibly forming complex, and (6) the ligand/receptor ratio. As an example of a typical application of the STD-NMR experiment we have also simulated the STD effects for a hypothetical trisaccharide bound to a protein. The CORCEMA theory for INOE and the associated algorithm are useful in a quantitative interpretation of the intensity changes in the ligand in both the STD-NMR and ICS-NMR, provided the identity of the receptor protons experiencing direct RF saturation is known. The formalism presented here is likely to be useful in the design of bioactive ligands to a specific target protein and in the quantitative mapping of binding epitopes and interfaces between molecules in complexes.
Collapse
Affiliation(s)
- V Jayalakshmi
- Department of Biochemistry and Molecular Genetics, NMR Core Facility, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294-2041, USA
| | | |
Collapse
|
33
|
Xu Y, Jablonsky MJ, Jackson PL, Braun W, Krishna NR. Automatic assignment of NOESY cross peaks and determination of the protein structure of a new world scorpion neurotoxin using NOAH/DIAMOD. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 148:35-46. [PMID: 11133274 DOI: 10.1006/jmre.2000.2220] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The 3D NMR structures of the scorpion neurotoxin, CsE-v5, were determined from the same NOESY spectra with NOAH/DIAMOD, an automated assignment and 3D structure calculation software package, and with a conventional manual assignment combined with a distance geometry/simulated annealing (X-PLOR) refinement method. The NOESY assignments and the 3D structures obtained from the two independent methods were compared in detail. The NOAH/DIAMOD program suite uses feedback filtering and self-correcting distance geometry methods to automatically assign NOESY spectra and to calculate the 3D structure of a protein. NOESY cross peaks were automatically picked using a standard software package and combined with 74 manually assigned NOESY peaks to start the NOAH/DIAMOD calculations. After 63 NOAH/DIAMOD cycles, using REDAC procedures in the last 8 cycles, and final FANTOM constrained energy minimization, a bundle of 20 structures with the smallest target functions has a RMSD of 0.81 A for backbone atoms and 1.11 A for all heavy atoms to the mean structure. Despite some missing chemical shifts of side chain protons, 776 (including 74 manually assigned) of 1130 NOE peaks were unambiguously assigned, 150 peaks have more than one possible assignment compatible with the bundle structures, and only 30 peaks could not be assigned within the given chemical shift tolerance ranges in either the D1 or the D2 dimension. The remaining 174, mainly weak NOE peaks were not compatible with the final 20 best bundle structures at the last NOAH/DIAMOD cycle. The automatically determined structures agree well with the structures determined independently using the conventional method and the same NMR spectra, with the mean RMSD in well-defined regions of 0.84 A for bb and 1.48 A for all heavy atoms from residues 2-5, 18-26, 32-36, and 39-45. This study demonstrates the potential of the NOAH/DIAMOD program suite to automatically assign NMR data for proteins and determine their structure.
Collapse
Affiliation(s)
- Y Xu
- Department of Human Biological Chemistry and Genetics, Sealy Center for Structural Biology, Galveston, Texas, 77555-1157, USA
| | | | | | | | | |
Collapse
|
34
|
Mihailescu D, Smith JC. Atomic detail peptide-membrane interactions: molecular dynamics simulation of gramicidin S in a DMPC bilayer. Biophys J 2000; 79:1718-30. [PMID: 11023880 PMCID: PMC1301066 DOI: 10.1016/s0006-3495(00)76424-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Molecular dynamics simulations have been performed of the sequence-symmetric cyclic decapeptide antibiotic gramicidin S (GS), in interaction with a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer, and the results compared with a "control" simulation of the system in the absence of GS. Following experimental evidence, the GS was initially set in a single antiparallel beta-sheet conformation with two Type II' beta-turns in an amphiphilic interaction with the membrane. This conformation and position remained in the 6.5 ns simulation. Main-chain dihedrals are on average approximately 26 degrees from those determined by NMR experiment on GS in dimethylsulfoxide (DMSO) solution. Sequence-symmetric main-chain and side-chain dihedral angle pairs converge to within approximately 5 degrees and approximately 10 degrees, respectively. The area per lipid, lipid tail order parameters, and quadrupole spin-lattice relaxation times of the control simulation are mostly in good agreement with corresponding experiments. The GS has little effect on the membrane dipole potential or water permeability. However, it is found to have a disordering effect (in agreement with experiment) and a fluidifying effect on lipids directly interacting with it, and an ordering effect on those not directly interacting.
Collapse
Affiliation(s)
- D Mihailescu
- Faculty of Biology, University of Bucharest, 76201 Bucharest, Romania
| | | |
Collapse
|
35
|
Mihailescu D, Smith JC. Molecular Dynamics Simulation of the Cyclic Decapeptide Antibiotic, Gramicidin S, in Dimethyl Sulfoxide Solution. J Phys Chem B 1999. [DOI: 10.1021/jp983674t] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dan Mihailescu
- SBPM, DBCM, Commissariat à L'Energie Atomique, CEA-Saclay, 911191, Gif-sur-Yvette, France, Faculty of Biology, University of Bucharest, Spl. Independentei, 91-95, 76201, Bucharest, Romania, and Lehrstuhl für Biocomputing, IWR, Universität Heidelberg, D-69120, Heidelberg, Germany
| | - Jeremy C. Smith
- SBPM, DBCM, Commissariat à L'Energie Atomique, CEA-Saclay, 911191, Gif-sur-Yvette, France, Faculty of Biology, University of Bucharest, Spl. Independentei, 91-95, 76201, Bucharest, Romania, and Lehrstuhl für Biocomputing, IWR, Universität Heidelberg, D-69120, Heidelberg, Germany
| |
Collapse
|
36
|
Curto EV, Moseley HN, Krishna NR. CORCEMA evaluation of the potential role of intermolecular transferred NOESY in the characterization of ligand-receptor complexes. J Comput Aided Mol Des 1996; 10:361-71. [PMID: 8951648 DOI: 10.1007/bf00124470] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report a theoretical characterization of the intermolecular transferred NOESY (inter-TrNOESY) between ligands and receptor macromolecules that bind reversibly, using a COmplete Relaxation and Conformational Exchange MAtrix (CORCEMA) theory developed in our laboratory. We examine the dependence of inter-TrNOESY on the dissociation constant, off-rate, ligand-to-receptor ratio, and distance variations between protons of interacting species within the complex. These factors are analyzed from simulations on two model systems: (i) neuraminidase complexed to a transition-state analogue; and (ii) thermolysin complexed to a leucine-based inhibitor. The latter case utilizes a three-state model of interaction to simulate the effect of hinge-bending motions on the inter-TrNOESY. Our calculations suggest a potential role for inter-TrNOESY (when observable) and CORCEMA analysis in properly docking the ligand within the active site, and in refining the conformation of the ligand-receptor (active-site) complex. These findings have implications on the structure-based design of ligands (e.g., inhibitors) reversibly binding to receptors (e.g., enzymes).
Collapse
Affiliation(s)
- E V Curto
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham 35294-2041, USA
| | | | | |
Collapse
|
37
|
Scheraga HA. Recent developments in the theory of protein folding: searching for the global energy minimum. Biophys Chem 1996; 59:329-39. [PMID: 8672720 DOI: 10.1016/0301-4622(95)00126-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Statistical mechanical theories and computer simulation are being used to gain an understanding of the fundamental features of protein folding. A major obstacle in the computation of protein structures is the multiple-minima problem arising from the existence of many local minima in the multidimensional energy landscape of the protein. This problem has been surmounted for small open-chain and cyclic peptides, and for regular-repeating sequences of models of fibrous proteins. Progress is being made in resolving this problem for globular proteins.
Collapse
Affiliation(s)
- H A Scheraga
- Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, USA
| |
Collapse
|