1
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Southern SA, Perras FA. Comparison of methods for the NMR measurement of motionally averaged dipolar couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 364:107710. [PMID: 38901172 DOI: 10.1016/j.jmr.2024.107710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
Motionally averaged dipolar couplings are an important tool for understanding the complex dynamics of catalysts, polymers, and biomolecules. While there is a plethora of solid-state NMR pulse sequences available for their measurement, in can be difficult to gauge the methods' strengths and weaknesses. In particular, there has not been a comprehensive comparison of their performance in natural abundance samples, where 1H homonuclear dipolar couplings are important and the use of large MAS rotors may be required for sensitivity reasons. In this work, we directly compared some of the more common methods for measuring C-H dipolar couplings in natural abundance samples using L-alanine (L-Ala) and the N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLF) tripeptide as model systems. We evaluated their performance in terms of accuracy, resolution, sensitivity, and ease of implementation. We found that, despite the presence of 1H homonuclear dipolar interactions, all methods, with the exception of REDOR, were able to yield the reasonable dipolar coupling strengths for both mobile and static moieties. Of these methods, PDLF provides the most convenient workflow and precision at the expense of low sensitivity. In low-sensitivity cases, MAS-PISEMA and DIPSHIFT appear to be the better options.
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Affiliation(s)
- Scott A Southern
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA
| | - Frédéric A Perras
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA; Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
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2
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Jain MG, Rajalakshmi G, Agarwal V, Madhu PK, Mote KR. On the direct relation between REDOR and DIPSHIFT experiments in solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106563. [PMID: 31353014 DOI: 10.1016/j.jmr.2019.07.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Rotational-echo double resonance (REDOR) and Dipolar-coupling chemical-shift correlation (DIPSHIFT) are commonly used experiments to probe heteronuclear dipole-dipole couplings between isolated pairs of spin-12 nuclei in magic-angle-spinning (MAS) solid-state NMR. Their widespread use is due to their robustness to experimental imperfections and a straightforward interpretation of data. Both of these experiments use rotor-synchronised π pulses to recouple the heteronuclear dipole-dipole couplings, and the observed intensity of resonances is modulated by a recoupled phase factor depending on the position or duration of the recoupling pulses. Several modifications to both of these experiments have been proposed, for example, the development of DIPSHIFT which employs strategies that mimic the multi-rotor-period nature of REDOR. We show here that REDOR and DIPSHIFT are in fact alternate implementations of the same experiment. The overt similarity in the design of REDOR and DIPSHIFT is also reflected in their theoretical description. Dipolar dephasing curves in REDOR are obtained by increasing the recoupling duration whilst keeping the position of the pulses constant, which results in a dephasing factor that is a function of only the dephasing time. DIPSHIFT, on the other hand, is a constant-time version of REDOR; the dipolar dephasing is a function of the position of the pulses with respect to the rotor period. We discuss the advantages and disadvantages of each implementation and suggest domains of applicability for these sequences.
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Affiliation(s)
- Mukul G Jain
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India
| | - G Rajalakshmi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India.
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India.
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3
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Markin AV, Markhasin E, Sologubov S, Smirnova NN, Griffin RG. Standard Thermodynamic Functions of Tripeptides N-Formyl-l-methionyl-l-leucyl-l-phenylalaninol and N-Formyl-l-methionyl-l-leucyl-l-phenylalanine Methyl Ester. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2014; 59:1240-1246. [PMID: 24803685 PMCID: PMC3993880 DOI: 10.1021/je400879v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
The heat capacities of tripeptides N-formyl-l-methionyl-l-leucyl-l-phenylalaninol (N-f-MLF-OH) and N-formyl-l-methionyl-l-leucyl-l-phenylalanine methyl ester (N-f-MLF-OMe) were measured by precision adiabatic vacuum calorimetry over the temperature range from T = (6 to 350) K. The tripeptides were stable over this temperature range, and no phase change, transformation, association, or thermal decomposition was observed. The standard thermodynamic functions: molar heat capacity Cp,m, enthalpy H(T) - H(0), entropy S(T), and Gibbs energy G(T) - H(0) of peptides were calculated over the range from T = (0 to 350) K. The low-temperature (T ≤ 50 K) heat capacities dependencies were analyzed using the Debye's and the multifractal theories. The standard entropies of formation of peptides at T = 298.15 K were calculated.
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Affiliation(s)
- Alexey V. Markin
- Lobachevsky
State University of Nizhni Novgorod, 23/5 Gagarin Avenue, 603950, Nizhni Novgorod, Russia
| | - Evgeny Markhasin
- Massachusetts
Institute of Technology, 150 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Semen
S. Sologubov
- Lobachevsky
State University of Nizhni Novgorod, 23/5 Gagarin Avenue, 603950, Nizhni Novgorod, Russia
| | - Natalia N. Smirnova
- Lobachevsky
State University of Nizhni Novgorod, 23/5 Gagarin Avenue, 603950, Nizhni Novgorod, Russia
| | - Robert G. Griffin
- Massachusetts
Institute of Technology, 150 Albany Street, Cambridge, Massachusetts 02139, United States
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4
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Gortari ID, Portella G, Salvatella X, Bajaj VS, van der Wel PCA, Yates JR, Segall MD, Pickard CJ, Payne MC, Vendruscolo M. Time Averaging of NMR Chemical Shifts in the MLF Peptide in the Solid State. J Am Chem Soc 2010; 132:5993-6000. [DOI: 10.1021/ja9062629] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Itzam De Gortari
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Guillem Portella
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Xavier Salvatella
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Vikram S. Bajaj
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Patrick C. A. van der Wel
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Jonathan R. Yates
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Matthew D. Segall
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Chris J. Pickard
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Mike C. Payne
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Michele Vendruscolo
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
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5
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Bajaj VS, van der Wel PC, Griffin RG. Observation of a low-temperature, dynamically driven structural transition in a polypeptide by solid-state NMR spectroscopy. J Am Chem Soc 2009; 131:118-28. [PMID: 19067520 PMCID: PMC2651395 DOI: 10.1021/ja8045926] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At reduced temperatures, proteins and other biomolecules are generally found to exhibit dynamic as well as structural transitions. This includes a so-called protein glass transition that is universally observed in systems cooled between 200 and 230 K, and which is generally attributed to interactions between hydrating solvent molecules and protein side chains. However, there is also experimental and theoretical evidence for a low-temperature transition in the intrinsic dynamics of the protein itself, absent any solvent. Here, we use low-temperature solid-state NMR to examine site-specific fluctuations in atomic structure and dynamics in the absence of solvents. In particular, we employ magic angle spinning NMR to examine a structural phase transition associated with dynamic processes in a solvent-free polypeptide, N-f-MLF-OH, lattice at temperatures as low as 90 K. This transition is characterized by the appearance of an extra set of lines in 1D (15)N spectra as well as additional cross peaks in 2D (13)C-(13)C and (13)C-(15)N spectra. Interestingly, the gradual, temperature-dependent appearance of the new spectral component is not accompanied by the line broadening typical of dynamic transitions. A direct comparison between the spectra of N-f-MLF-OH and the analog N-f-MLF-OMe, which does not display this transition, indicates a correlation of the structural transition to the temperature dependent motion of the aromatic phenylalanine side chain. Several quantitative solid state NMR experiments were employed to provide site-specific measurements of structural and motional features of the observed transition.
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Affiliation(s)
| | | | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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6
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TORRINI I, ZECCHINI GPAGANI, PARADISI MPAGLIALUNGA, LUCENTE G, GAVUZZO E, MAZZA F, POCHETTI G, SPISANF S, GIULIANI A. Synthesis and properties of chemotactic peptide analogs. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1991.tb01532.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Selvatici R, Falzarano S, Mollica A, Spisani S. Signal transduction pathways triggered by selective formylpeptide analogues in human neutrophils. Eur J Pharmacol 2006; 534:1-11. [PMID: 16516193 DOI: 10.1016/j.ejphar.2006.01.034] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 01/03/2006] [Accepted: 01/20/2006] [Indexed: 01/01/2023]
Abstract
Human neutrophils are highly specialised for their primary function, i.e. phagocytosis and destruction of microorganisms. Leukocyte recruitment to sites of inflammation and infection is dependent upon the presence of a gradient of locally produced chemotactic factors. The bacterial peptide N-formyl-methionyl-leucyl-phenylalanine (fMLP) was one of the first of these to be identified and is a highly potent leukocyte chemoattractant. It interacts with its receptor on the neutrophil membrane, activating these cells through a G-protein-coupled pathway. Two functional fMLP receptors have thus far been cloned and characterized, namely FPR (formyl peptide receptor) and FPRL1 (FPR like-1), with high and low affinities for fMLP, respectively. FMLP is known to activate phospholipase C (PLC), PLD, PLA2 and phosphatidylinositol-3-kinase (PI3K), and it also activates tyrosine phosphorylation. The second messengers resulting from the fMLP receptor interaction act on various intracellular kinases, including protein kinase C (PKC) and mitogen-activated protein kinases (MAPKs). The activation of these signal transduction pathways is known to be responsible for various biochemical responses which contribute to physiological defence against bacterial infection and cell disruption. This review will consider the ability of selective analogues (ligands able to discriminate between different biological responses) to activate a single spectrum of signal transduction pathways capable of producing a unique set of cellular responses, hypothesising that a distinctive imprint of signal protein activation may exist. Through more complete understanding of intracellular signaling, new drugs could be developed for the selective inflammatory blockade.
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Affiliation(s)
- Rita Selvatici
- Dipartimento di Medicina Sperimentale e Diagnostica, Sezione Genetica Medica, Via Fossato di Mortara 74, Università degli Studi di Ferrara, 44100 Ferrara, Italy
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8
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Tyndall JDA, Pfeiffer B, Abbenante G, Fairlie DP. Over One Hundred Peptide-Activated G Protein-Coupled Receptors Recognize Ligands with Turn Structure. Chem Rev 2005; 105:793-826. [PMID: 15755077 DOI: 10.1021/cr040689g] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joel D A Tyndall
- Center for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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9
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Rathore RS. Conformational investigations on analogs of inflammation response inducing chemotactic tripeptide fMLP. Biopolymers 2005; 80:651-64. [PMID: 15648091 DOI: 10.1002/bip.20231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Conformations of three analogs of for-L-Met-L-Leu-L-Phe-OH (fMLP), which initiates inflammatory response by interaction with the formyl peptide receptor (FPR), have been investigated by the application of the X-ray crystallographic technique. The investigated analogs of fMLP peptides are as follows: for-L-Met-1-amino-1-cyclooctane-carbonyl(Ac8c)-L-Phe-OMe; for-L-Met-L-Leu-L-p-iodo-Phe-OH; and for-L-Met-di-n-propylglycyl(Dpg)-L-Phe-OMe. The peptide backbone in and is constrained at position of fMLP by the introduction of Calpha,alpha-disubstituted glycines. In peptide, Phe-OMe is substituted by p-iodo-Phe-OH. Crystal structures reveal an overall folded conformation adopted by and. The former is folded in the type II beta-turn, which is stabilized by an intramolecular 1<--4 (formyl) C==O...H--N (Phe) hydrogen bond, whereas the latter is folded in an open turn without any intramolecular hydrogen bond. On the other hand, peptide has an extended conformation, and two different molecules in a crystallographic asymmetric unit form an antiparallel beta-sheet-like structure. In and, residues Ac8c and Dpg adopt left-handed helical and fully extended (C5) conformations, respectively. The cyclooctane ring in Ac8c acquires a boat-chair conformation. Crystal packing of is characterized by the association of aliphatic-aromatic rings via a C--H...pi interaction. In the crystal of, contrary to the usual observations, peptides are interlinked via networks of head-to-tail hydrogen bond and pi...pi interactions, which are generally observed to be mutually exclusive. The structure-function mechanism of the ligand-receptor interaction is discussed.
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10
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Rienstra CM, Tucker-Kellogg L, Jaroniec CP, Hohwy M, Reif B, McMahon MT, Tidor B, Lozano-Pérez T, Griffin RG. De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A 2002; 99:10260-5. [PMID: 12149447 PMCID: PMC124901 DOI: 10.1073/pnas.152346599] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2002] [Accepted: 06/10/2002] [Indexed: 11/18/2022] Open
Abstract
The three-dimensional structure of the chemotactic peptide N-formyl-l-Met-l-Leu-l-Phe-OH was determined by using solid-state NMR (SSNMR). The set of SSNMR data consisted of 16 (13)C-(15)N distances and 18 torsion angle constraints (on 10 angles), recorded from uniformly (13)C,(15)N- and (15)N-labeled samples. The peptide's structure was calculated by means of simulated annealing and a newly developed protocol that ensures that all of conformational space, consistent with the structural constraints, is searched completely. The result is a high-quality structure of a molecule that has thus far not been amenable to single-crystal diffraction studies. The extensions of the SSNMR techniques and computational methods to larger systems appear promising.
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Affiliation(s)
- Chad M Rienstra
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Ladizhansky V, Veshtort M, Griffin RG. NMR determination of the torsion angle psi in alpha-helical peptides and proteins: the HCCN dipolar correlation experiment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 154:317-324. [PMID: 11846590 DOI: 10.1006/jmre.2001.2488] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Several existing methods permit measurement of the torsion angles phi, psi and chi in peptides and proteins with solid-state MAS NMR experiments. Currently, however, there is not an approach that is applicable to measurement of psi in the angular range -20 degree to -70 degree, commonly found in alpha-helical structures. Accordingly, we have developed a HCCN dipolar correlation MAS experiment that is sensitive and accurate in this regime. An initial REDOR driven (13)C'--(15)N dipolar evolution period is followed by the C' to C(alpha) polarization transfer and by Lee--Goldburg cross polarization recoupling of the (13)C(alpha)(1)H dipolar interaction. The difference between the effective (13)C(1)H and (13)C(15)N dipolar interaction strengths is balanced out by incrementing the (13)C--(15)N dipolar evolution period in steps that are a factor of R(R approximately omega(CH)/omega(CN)) larger than the (13)C--(1)H steps. The resulting dephasing curves are sensitive to variations in psi in the angular region associated with alpha-helical secondary structure. To demonstrate the validity of the technique, we apply it to N-formyl-[U-(13)C,(15)N] Met-Leu-Phe-OH (MLF). The value of psi extracted is consistent with the previous NMR measurements and close to that reported in diffraction studies for the methyl ester of MLF, N-formyl-[U-(13)C,(15)N]Met-Leu-Phe-OMe.
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Affiliation(s)
- Vladimir Ladizhansky
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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12
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Reif B, Hohwy M, Jaroniec CP, Rienstra CM, Griffin RG. NH-NH vector correlation in peptides by solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 145:132-141. [PMID: 10873504 DOI: 10.1006/jmre.2000.2067] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a novel solid-state magic angle-spinning NMR method for measuring the NH(i)-NH(i+1) projection angle θ(i,i+1) in peptides. The experiment is applicable to uniformly (15)N-labeled peptides and is demonstrated on the chemotactic tripeptide N-formyl-l-Met-l-Leu-l-Phe. The projection angle θ(i,i+1) is directly related to the peptide backbone torsion angles φ(i) and psi(i). The method utilizes the T-MREV recoupling scheme to restore (15)N-(1)H interactions, and proton-mediated spin diffusion to establish (15)N-(15)N correlations. T-MREV has recently been shown to increase the dynamic range of the (15)N-(1)H recoupling by gamma-encoding, and permits an accurate determination of the recoupled NH dipolar interaction. The results are interpreted in a quasi-analytical fashion that permits efficient extraction of the structural parameters.
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Affiliation(s)
- B Reif
- Department of Chemistry and MIT/Harvard Center for Magnetic Resonance, Cambridge, Massachusetts, 02139, USA
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13
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Torrini I, Zecchini GP, Paradisi MP, Lucente G, Mastropietro G, Gavuzzo E, Mazza F, Pochetti G, Traniello S, Spisani S. Modified chemotactic peptides: Synthesis, conformation, and activity of HCO-Thp-Ac6c-Phe-OMe. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199609)39:3<327::aid-bip5>3.0.co;2-q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Prossnitz ER, Ye RD. The N-formyl peptide receptor: a model for the study of chemoattractant receptor structure and function. Pharmacol Ther 1997; 74:73-102. [PMID: 9336017 DOI: 10.1016/s0163-7258(96)00203-3] [Citation(s) in RCA: 219] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
N-formyl peptides, such as fMet-Leu-Phe, are one of the most potent chemoattractants for phagocytic leukocytes. The interaction of N-formyl peptides with their specific cell surface receptors has been studied extensively and used as a model system for the characterization of G-protein-coupled signal transduction in phagocytes. The cloning of the N-formyl peptide receptor cDNA from several species and the identification of homologous genes have allowed detailed studies of structural and functional aspects of the receptor. Recent findings that the receptor is expressed in nonhematopoietic cells and that nonformylated peptides can activate the receptor suggest potentially novel functions and the existence of additional ligands for this receptor.
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MESH Headings
- Amino Acid Sequence
- Animals
- Chemotactic Factors/metabolism
- Humans
- Models, Biological
- Molecular Sequence Data
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/physiology
- Receptors, Formyl Peptide
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Immunologic/physiology
- Receptors, Peptide/chemistry
- Receptors, Peptide/genetics
- Receptors, Peptide/physiology
- Sequence Homology, Amino Acid
- Structure-Activity Relationship
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Affiliation(s)
- E R Prossnitz
- Department of Immunology, Scripps Research Institute, La Jolla, CA 92037, USA
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15
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Torrini I, Paglialunga Paradisi M, Pagani Zecchini G, Lucente G, Gavuzzo E, Mazza F, Pochetti G, Traniello S, Spisani S. Synthesis, conformation, and biological activity of two fMLP-OMe analogues containing the new 2-[2'-(methylthio)ethyl]methionine residue. Biopolymers 1997; 42:415-26. [PMID: 9283291 DOI: 10.1002/(sici)1097-0282(19971005)42:4<415::aid-bip5>3.0.co;2-t] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The new C alpha-tetrasubstituted alpha-amino acid residue 2-[2'-(methylthio)ethyl]methionine (Dmt) has been introduced into the reference chemotactic tripeptide HCO-Met-Leu-Phe-OMe (fMLP-OMe) in place of the leucine or methionine, respectively. The biological activity of the new analogues [Dmt2]fMLP-OMe (2) and [Dmt1]fMLP-OMe (3) has been determined; whereas 2 is active toward human neutrophils, stimulating directed migration, superoxide anion generation, and lysozyme release, 3 results practically inactive in all tested assays. A conformational analysis on 2 and 3 has been performed in solution by using ir absorption and 1H-nmr. The conformation of 2 was also examined in the crystal by x-ray diffraction methods. Both 2 and 3 adopt fully extended conformation in correspondence with the Dmt residue. Biological and conformational results are discussed and compared with related previously studied models.
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Affiliation(s)
- I Torrini
- Dipartimento di Studi Farmaceutici, Università La Sapienza, Roma, Italy
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16
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Torrini I, Pagani Zecchini G, Paglialunga Paradisi M, Lucente G, Mastropietro G, Gavuzzo E, Mazza F, Pochetti G, Traniello S, Spisani S. Modified chemotactic peptides: synthesis, conformation, and activity of HCO-Thp-Ac6c-Phe-OMe. Biopolymers 1996; 39:327-37. [PMID: 8756513 DOI: 10.1002/(sici)1097-0282(199609)39:3%3c327::aid-bip5%3e3.0.co;2-q] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
HCO-Thp-Ac6c-Phe-OMe (3) has been synthesized as a new analogue of the prototypical chemotactic agent HCO-Met-Leu-Phe-OMe (fMLP-OMe). Compound 3 contains 4-aminotetra-hydrothiopyran-4-carboxylic acid (Thp) and 1-aminocyclohexane-1-carboxylic acid (Ac6c) as achiral, conformationally restricted mimics of Met and Leu, respectively. In the crystal, the formyltripeptide adopts an helical conformation at the Thp and Ac6c residues, of the type alpha R and alpha L, respectively, whereas the C-terminal phenylalanine is quasi-extended. A system of two consecutive gamma-turns, centered at the first two residues, better explains the nmr data as compared with an alternative beta-turn structure. The conformation of the new analogue 3 is compared with those of two related peptides containing Thp as N-terminal residue. The biological activity of 3 has been determined on human neutrophils and compared to that of the previously studied model [Ac6c2] fMLP-OMe. While the above analogue is highly active in the superoxide anion production, the new tripeptide 3 is practically unable to elicit any of the tested biological activities.
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Affiliation(s)
- I Torrini
- Dipartimento di Studi Farmaceutici, Università La Sapienza, Roma, Italy
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17
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Conformational studies of chemotactic HCO-Met-Leu-Phe-OMe analogues. Amino Acids 1995; 9:375-83. [DOI: 10.1007/bf00807274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/1995] [Accepted: 08/10/1995] [Indexed: 11/27/2022]
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18
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Cavicchioni G, Vertuani G, Scatturin A, Spisani S. The role of peptide bond in chemotactic for-met-leu-phe-ome focused by depsipeptide analogs. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80564-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Torrini I, Pagani Zecchini G, Paglialunga Paradisi M, Lucente G, Gavuzzo E, Mazza F, Pochetti G, Traniello S, Spisani S. Modified chemotactic peptides: synthesis, crystal conformation, and activity of For-Hse(Me)-Leu-Phe-OMe. Biopolymers 1994; 34:1-9. [PMID: 8110962 DOI: 10.1002/bip.360340102] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The presence of the sulfur atom of the methionine side chain exerts significant effects at different levels on biochemical behavior of chemotactic N-formylpeptides. In order to acquire more information on this point, the synthesis, the conformation in the crystal, and the activity of For-Hse(Me)-Leu-Phe-OMe (2)--an oxygen analogue of For-Met-Leu-Phe-OMe (fMLP-OMe) containing the O-methyl-L-homoserine in place of the native methionine at position 1--is reported. The new analogue 2 adopts a conformation that is extended at the first two residues and folded at the C-terminal phenylalanine. This conformation is different from that of the parent fMLP-OMe and strikingly similar to that adopted by fMLP-OBu(t). The side-chain spatial orientation of 2 corresponds to that adopted by fMLP-OH when cocrystallized with an immunoglobulin possessing binding properties similar to those of neutrophil receptors. When tested on human neutrophils the formylpeptide 2 is more active than the parent in the stimulation of directed mobility and maintains both the granule enzyme release activity and the superoxide anion production.
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Affiliation(s)
- I Torrini
- Dipartimento di Studi Farmaceutici, Università La Sapienza, Roma, Italy
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20
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Quehenberger O, Prossnitz E, Cavanagh S, Cochrane C, Ye R. Multiple domains of the N-formyl peptide receptor are required for high-affinity ligand binding. Construction and analysis of chimeric N-formyl peptide receptors. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(17)46825-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Di Blasio B, Pavone V, Lombardi A, Pedone C, Benedetti E. Noncoded residues as building blocks in the design of specific secondary structures: symmetrically disubstituted glycines and beta-alanine. Biopolymers 1993; 33:1037-49. [PMID: 8343584 DOI: 10.1002/bip.360330706] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Structural changes can be induced in a peptide by selective substitution of coded alpha-amino acid residues by noncoded alpha-amino acid residues and the consequent production of analogues with modified structure and conformational preferences. In this review article we summarize the solid state structural results and the conformational preferences of two classes of "building blocks": (a) the linear and cyclic symmetrically alpha, alpha-disubstituted glycines in which either two identical n-alkyl groups replace the hydrogen atoms of the glycine residue or a cyclic aliphatic side-chain system is formed by linking the two alpha-carbon side chains, respectively; and (b) the beta-alanine residue. Examples, whenever possible, of the use of these residues for the elucidation of the bioactive conformation in the appropriate biological systems will be given.
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Affiliation(s)
- B Di Blasio
- Department of Chemistry, University of Naples Federico II, Italy
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22
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Dugas H, Laroche M, Ptak M, Labbé H. Synthesis, biological activity, conformational analysis by NMR and molecular modeling of N-formyl-L-Met-L-Pro-L-Phe-OMe, a proline analogue of the chemotactic peptide N-formyl-L-Met-L-Leu-L-Phe-OH. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1993; 41:595-605. [PMID: 8394292 DOI: 10.1111/j.1399-3011.1993.tb00482.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The tripeptide N-formyl-Met-Pro-Phe-OMe (f-MPF-OMe), an analogue of the signal peptide N-formyl-Met-Leu-Phe-OH (f-MLF-OH), was synthesized and its chemotactic activity evaluated; it showed no activity in either superoxide production or calcium mobility with human neutrophils. However, the corresponding acid f-MPF-OH retained about 25% activity in the production of superoxide. The conformation of the f-MPF-OMe analogue was evaluated by NMR spectroscopy and molecular simulation and shown to predominate in a gamma-turn with a hydrogen bond between Met CO and Phe NH. Since this analogue is not chemotactic, it is suggested that for recognition the receptor prefers a peptide with a flexible backbone, favoring an extended conformation in the binding site.
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Affiliation(s)
- H Dugas
- Department of Chemistry, University of Montreal, Quebec, Canada
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23
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Pagani Zecchini G, Paglialunga Paradisi M, Torrini I, Lucente G, Gavuzzo E, Mazza F, Pochetti G, Paci M, Sette M, Di Nola A. Synthesis, conformation, and activity of HCO-Met-delta Z Leu-Phe-OMe, an active analogue of chemotactic N-formyltripeptides. Biopolymers 1993; 33:437-51. [PMID: 8461452 DOI: 10.1002/bip.360330310] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In order to induce a beta-turn conformation into the chemotactic linear tripeptide N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLP), the new analogue N-formyl-L-methionyl-delta Z leucyl-L-phenylalanine methyl ester [delta Z Leu]2fMLP-OMe (1) has been synthesized. The conformational and biochemical consequences of this chemical modification have been determined. Analogue 1 has been synthesized by using N-carboxy-(Z)-alpha,beta-didehydroleucine anhydride as key compound to introduce the unsaturated residue at the central position of the tripeptide 1. The x-ray analysis shows that 1 adopts in the crystal a type II beta-turn conformation in which the new residue occupies the (i + 2) position, and an intramolecular H bond is formed between the formylic oxygen and the Phe NH. 1H-nmr analysis based on nuclear Overhauser effect measurements suggests that the same folded conformation is preferred in CDCl3 solution; this finding is also supported by molecular dynamics simulation. The biological activity of 1 has been determined on human neutrophils (polymorphonuclear leukocytes) and compared to that shown by fMLP-OMe. Chemotactic activity, granule enzyme release, and superoxide anion production have been determined. Analogue 1 is practically inactive as chemoattractant, highly active in the superoxide generation, and similar to the parent in the lysozyme release. The conformational restriction imposed on the backbone by the presence of the unsaturated residue is discussed in relation with the observed bioselectivity.
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Affiliation(s)
- G Pagani Zecchini
- Dipartimento di Studi Farmaceutici, Università La Sapienza, Roma, Italy
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24
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Srikrishnan T, Parthasarathy R. Conformation and hydrogen bonding of N-formylpeptides: crystal and molecular structure of N-formyl-L-alanyl-L-aspartic acid. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1991; 38:335-9. [PMID: 1797707 DOI: 10.1111/j.1399-3011.1991.tb01512.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Crystals of N-formyl-L-alanyl-L-aspartic acid (C8H11N2O6) grown from aqueous methanol solution are orthorhombic, space group, P2(1)2(1)2(1) with cell parameters at 294K of a = 13.619(2), b = 8.567(2), c = 9.583(3)A, V = 1118.1A3, M.W. = 232.2, Z = 4, Dm = 1.38 g/cm3 and Dx = 1.378 g/cm3. The crystal structure was solved by the application of direct methods and refined to an R value of 0.075 for 1244 reflections with I greater than or equal to 3 sigma collected on a CAD-4 diffractometer. The structure contains two short intermolecular hydrogen bonds: (i) between the C-terminal carboxyl OH and the N-acyl oxygen (2.624(3)A), a characteristic feature found in many N-acyl peptides and (ii) between the aspartic carboxyl OH. and the peptide oxygen OP1 (2.623(3)A). The peptide is nonplanar (omega = 165.5(6) degrees). The molecule takes up a folded conformation in contrast to N-formyl peptides which form extended beta-sheets; the values of phi 1, psi 1, phi 2, psi 2(1), and psi 2(2) are, respectively -65.7(6), 152.0(5), -107.2(5), 30.9(5), and -150.3(6). The aspartic acid side chain conformation is g- with chi 1 = 73.1(5). The formyl group, as expected, is transplanar [OF-CF-N1-CA1 = -4.0(8) degrees]. The presence of the short O-H ... O hydrogen bond emerges as a structural feature common to this peptide and several other N-formyl peptides. There are no C-H ... O hydrogen bonds in this structure.
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Affiliation(s)
- T Srikrishnan
- Biophysics Department, Roswell Park Cancer Institute, Buffalo, New York
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25
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Dentino A, Raj P, Bhandary K, Wilson M, Levine M. Role of peptide backbone conformation on biological activity of chemotactic peptides. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)55084-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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26
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Gavuzzo E, Lucente G, Mazza F, Zecchini GP, Paradisi MP, Pochetti G, Torrini I. Synthesis and properties of chemotactic peptide analogs. I. Crystal structure and molecular conformation of HCO-Met-leu-Ain-OMe. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1991; 37:268-76. [PMID: 1894442 DOI: 10.1111/j.1399-3011.1991.tb00739.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
HCO-Met-Leu-Ain-OMe (2), an analog of the chemotactic peptide HCO-Met-Leu-Phe-OH, containing the conformationally blocked residue of the 2-aminoindane-2-carboxylic acid (Ain) has been synthesized and its crystal and molecular conformation has been determined. Crystals of 2 are monoclinic, space group P2(1), with a = 15.059(7), b = 18.548(7), c = 9.600(4) A; beta = 85.04(3) degrees. The structure has been solved by direct methods and refined to R = 0.069 for 2813 independent reflections with I greater than 2.5 sigma (I). Two independent molecules A and B have been found in the asymmetric unit of the crystal of 2. Their conformation can be described as extended at the Met and Leu residues, but folded at the C-terminal Ain residue. The helical folding is left- and right-handed in the A and B molecule, respectively. The crystal packing is characterized by ribbons of intermolecular hydrogen bonded molecules extended along the c direction. The constrained analog 2 is highly active in the superoxide production, thus indicating that a stabilization of a helical folding at the C-terminal region of chemotactic tripeptides maintains the activity. The orientation of the aromatic ring, with respect to its adjacent backbone atoms, does not seem critical for the activity.
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Affiliation(s)
- E Gavuzzo
- Institute of Structural Chemistry, G. Giacomello CNR, Monterotondo Stazione, Rome, Italy
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27
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Zecchini GP, Paradisi MP, Torrini I, Lucente G, Gavuzzo E, Mazza F, Pochetti G, Spisani S. For-Met-ΔzLeu-Phe-OMe: A new active analog of chemotactic N-formyltripeptides with β-turn crystal conformation. Tetrahedron Lett 1991. [DOI: 10.1016/s0040-4039(00)92174-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Benedetti E. X-ray crystallography of peptides: the contributions of the Italian laboratories. Biopolymers 1996; 40:3-44. [PMID: 8541447 DOI: 10.1002/(sici)1097-0282(1996)40:1<3::aid-bip2>3.0.co;2-#] [Citation(s) in RCA: 131] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The review article summarizes the most relevant solid state structural and conformational results obtained in the laboratories involved in Italy in the studies of synthetic and natural peptides by x-ray diffraction analyses. Some of the topics will include research studies carried out in other European countries, whereas in other cases studies carried out in Italy will be included in other review articles included in this volume. The review deals with peptides containing symmetrically achiral and unsymmetrically chiral C alpha,alpha-dialkylated glycine residues, peptides containing beta-alanine residues, alpha,beta-dehydroamino acid residues, and aminosuccinyl residues, peptides containing the thioamide surrogate, heterochiral peptides and several bioactive peptides systems with the proposed relationships between function and structure.
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Affiliation(s)
- E Benedetti
- Biocrystallography Centre, CNR, University of Napoli Federico II, Italy
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