Conformations of Prolyl–Peptide Bonds in the Bradykinin 1–5 Fragment in Solution and in the Gas Phase

Voronina, Liudmila; Masson, Antoine; Kamrath, Michael Z.; Schubert, Franziska; Clemmer, David E.; Baldauf, Carsten; Rizzo, Thomas R.

doi:10.1021/jacs.6b04550

Cited by 59 publications

(61 citation statements)

References 91 publications

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“…Bradykinin binds to its receptors in an open geometry where all the Pro 2,3,8 are in the trans conformational structure. Recently, Clemmer's group deconvoluted several conformational structures of BK in different solution composition by using IMS‐MS and established that cis ↔ trans isomerization of prolyl‐peptide bonds is key for different conformations . The interaction of BK with different metal cations viz., alkali, alkaline, and transition metals, was investigated extensively by using tandem MS along with DFT calculations to determine their respective binding site.…”

Section: [Bradykinin‐(n‐1)h + Ncui] and [Bradykinin‐(2n‐1)h + Ncuii];mentioning

confidence: 99%

Binding of Cu⁺ and Cu²⁺ with peptides: Peptides = oxytocin, Arg⁸‐vasopressin, bradykinin, angiotensin‐I, substance‐P, somatostatin, and neurotensin

2018

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The intrinsic binding ability of 7 natural peptides (oxytocin, arg -vasopressin, bradykinin, angiotensin-I, substance-P, somatostatin, and neurotensin) with copper in 2 different oxidation states (Cu ) derived from different Cu precursor sources have been investigated for their charge-dependent binding characteristics. The peptide-Cu complexes, [M - (n-1)H + nCu ] and [M - (2n-1)H + nCu ], are prepared/generated by the reaction of peptides with CuI solution/Cu-target and CuSO solution and are analyzed by using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. The MALDI mass spectra of both [M - (n-1)H + nCu ] and [M - (2n-1)H + nCu ] complexes show no mass shift due to the loss of ─H atoms in the main chain ─NH of these peptides by Cu and Cu deprotonation. The measured m/z value indicates the reduction of Cu oxidation state into Cu during MALDI processes. The number and relative abundance of Cu bound to the peptides are greater compared with the Cu bound peptides. Oxytocin, arg -vasopressin, bradykinin, substance-P, and somatostatin show the binding of 5Cu , and angiotensin-I and neurotensin show the binding of 7Cu from both CuI and Cu targets, while bradykinin shows the binding of 2Cu , oxytocin, arg -vasopressin, angiotensin-I, and substance-P; somatostatin shows the binding of 3Cu ; and neurotensin shows 4Cu binding. The binding of more Cu with these small peptides signifies that the bonding characteristics of both Cu and Cu are different. The amino acid residues responsible for the binding of both Cu and Cu in these peptides have been identified based on the density functional theory computed binding energy values of Cu and the fragment transformation method predicted binding preference of Cu for individual amino acids.

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Section: [Bradykinin‐(n‐1)h + Ncui] and [Bradykinin‐(2n‐1)h + Ncuii];mentioning

confidence: 99%

Binding of Cu⁺ and Cu²⁺ with peptides: Peptides = oxytocin, Arg⁸‐vasopressin, bradykinin, angiotensin‐I, substance‐P, somatostatin, and neurotensin

2018

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“…[22][23][24] Further, IM-MS can be used to prepare samples for gas-phase IR spectroscopy. [25][26][27][28][29] Here ions are simultaneously mass-tocharge (m/z) selected by MS and specific oligomers are geometrical size selected by IMS. This is in contrast to experiments where only m/z selection is used which can suffer from signal overlap between a cluster and its larger counterpart, which, for example, have twice the mass and twice the charge.…”

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confidence: 99%

Infrared spectrum and structure of the homochiral serine octamer–dichloride complex

et al. 2017

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The amino acid serine is known to form a very stable octamer which has properties that sets it apart from serine complexes having different sizes or from complexes composed of other amino acids. For example, both singly protonated serine octamers and anionic octamers complexed with two halogen ions, strongly prefer homochirality even when assembled from racemic D, L mixtures.Consequently, the structures of these complexes are of great interest but no acceptable candidates have so far been identified. Here we investigate anionic serine octamers coordinated with two chloride ions using a novel ion mobility/infrared spectroscopy technique in combination with theoretical calculations. The results allow the identification of a unique structure for (Ser 8 Cl 2 ) 2-that is highly symmetric, very stable, homochiral and whose calculated properties match those observed in the experiments. 3Clusters of atoms or molecules with unusually high relative intensities in mass spectra are termed "magic". In many instances, those "magic" clusters could be assigned to specific structures, often of high symmetry. Examples are numerous and include rare gas clusters 1 , fullerenes, most notably C 60 , 2 Ti 8 C 12 "metallocarbohedrane", 3 metal clusters such as Au 20 , 4,5 and highly symmetric protonated water clusters. 6,7 In the case of C 60 , the initial observation of magic numbers in mass spectra eventually led to the discovery of a new group of materials and a new form of carbon.Occasionally a "magic" cluster resists structural characterization. A famous example is the serine octamer. After electrospray of solutions containing serine, it was first observed that a cluster with the composition (Ser 8 H) + dominated the mass spectrum. 8 This is in contrast to mass spectra of other amino acid clusters, for which the intensity patterns of peaks in their mass spectra show much smoother evolution. The experimental observations have spurred calculations, and several candidates for structures of cationic serine octamers have been proposed. 8,17,[19][20][21] However, for most of them, the proposed structures do not provide an obvious reason for the observed homochirality. In addition, while the calculations indicate that the proposed structures are stable, they are not dramatically more stable compared to serine clusters of different sizes. Thus, there is no general consensus of the structure of serine octamer clusters and the quest for finding a structure that is compatible with the experimental observations is still ongoing. 4In contrast to the abundance of studies on the cationic serine octamer, little attention has so far been given to the anionic species. Here, we present results from a study on serine cluster anions, in which we couple ion mobility-mass spectrometry (IMS-MS) with infrared (IR) spectroscopy.IMS-MS gives the absolute, angle averaged collision cross section (CCS) of specific clusters and this value can be used to determine the overall size of the cluster and to judge if particular calculated structures are compa...

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“…For instance, Warnke et al 14 demonstrated that combining IM-MS and infrared multiple photon dissociation (IRMPD) spectroscopy reveals two distinct protomers of benzocaine, where depending on the protonation site (N or O), a unique N-H and O-H stretch frequencies appear. Similarly, Voronina et al 28 utilised IM-MS and cold-ion spectroscopy to study the bradykinin fragment (BK [1][2][3][4][5] 2+ ) ions elucidating cis-trans and trans-cis conformations for the more compact conformer and kinetically trapped trans-trans configuration for the larger conformer, highlighting the cis-trans isomerization of the peptide bonds during the desolvation process. In both cases, IM-MS data was supplemented with gas-phase IR experiments which in turn were supported by high-level calculations to assign potential in vacuo species.…”

Section: Mason-schamp Equation Whereas Travelling Wave Im-ms (Twims-mentioning

confidence: 99%

A Careful Consideration of the Influence of Structure, Partial charges and Basis Sets on Collision Cross Sections of Monosaccharides when Comparing Values from DFT Calculated Conformers to those Obtained Experimentally

Migas

Gray

Flitsch

et al. 2017

Preprint

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Molecular modelling is routinely employed to assign 3D structures to collision cross sections (CCSs) derived from ion mobility mass spectrometry experiments (IM-MS). The assignment of model structures to the experimental CCSs remains an ambiguous task, where one of several methods may be used to obtain a CCS from a given set of coordinates. The most reliable of the commonly used techniques, the Trajectory Method, starts with atomic coordinates which can be accompanied by partial atomic charges, obtained using ab initio methods. Here, we use lithiated α-and β-glucose ions as exemplar molecules to detect the effect conformational modification and changes to the partial charge distribution have on computed collision cross sections. Six popular charge schemes (Mulliken, APT, CHelpG, MK, HLY and NPA) were examined in combination with three functionals (Hartree-Fock, B3LYP and M05) and five basis sets (STO-3G, 3-21G, 6-31G, 6-31+G and 6-31G*) on twenty unique structures.Our findings indicate that molecular conformation makes a significant contribution to fluctuations of partial charges in Electrostatic Potential (ESP) and Mulliken charge scheme; Partial charges derived using Natural Population Analysis (NPA) and ESP methods are largely independent of functional and basis set selection; and both selection of the charge scheme and functional/basis set combination play a large role in the resultant CCS, often causing few percent fluctuations in the computed values.

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Conformations of Prolyl–Peptide Bonds in the Bradykinin 1–5 Fragment in Solution and in the Gas Phase

Cited by 59 publications

References 91 publications

Binding of Cu⁺ and Cu²⁺ with peptides: Peptides = oxytocin, Arg⁸‐vasopressin, bradykinin, angiotensin‐I, substance‐P, somatostatin, and neurotensin

Binding of Cu⁺ and Cu²⁺ with peptides: Peptides = oxytocin, Arg⁸‐vasopressin, bradykinin, angiotensin‐I, substance‐P, somatostatin, and neurotensin

Infrared spectrum and structure of the homochiral serine octamer–dichloride complex

A Careful Consideration of the Influence of Structure, Partial charges and Basis Sets on Collision Cross Sections of Monosaccharides when Comparing Values from DFT Calculated Conformers to those Obtained Experimentally

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Conformations of Prolyl–Peptide Bonds in the Bradykinin 1–5 Fragment in Solution and in the Gas Phase

Cited by 59 publications

References 91 publications

Binding of Cu+ and Cu2+ with peptides: Peptides = oxytocin, Arg8‐vasopressin, bradykinin, angiotensin‐I, substance‐P, somatostatin, and neurotensin

Binding of Cu+ and Cu2+ with peptides: Peptides = oxytocin, Arg8‐vasopressin, bradykinin, angiotensin‐I, substance‐P, somatostatin, and neurotensin

Infrared spectrum and structure of the homochiral serine octamer–dichloride complex

A Careful Consideration of the Influence of Structure, Partial charges and Basis Sets on Collision Cross Sections of Monosaccharides when Comparing Values from DFT Calculated Conformers to those Obtained Experimentally

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Binding of Cu⁺ and Cu²⁺ with peptides: Peptides = oxytocin, Arg⁸‐vasopressin, bradykinin, angiotensin‐I, substance‐P, somatostatin, and neurotensin

Binding of Cu⁺ and Cu²⁺ with peptides: Peptides = oxytocin, Arg⁸‐vasopressin, bradykinin, angiotensin‐I, substance‐P, somatostatin, and neurotensin