Improved NOE fitting for flexible molecules based on molecular mechanics data – a case study with <i>S</i>-adenosylmethionine

Bame, Jessica R.; Hoeck, Casper Rønn; Carrington, M.J.; Jäger, Christof M.; Croft, Anna K.

doi:10.1039/c7cp07265a

Cited by 28 publications

(27 citation statements)

References 60 publications

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“…Principal Component Analysis (PCA) of the trajectory shows that the rotation around the glycosidic angle has the biggest contribution to the ligand’s flexibility as it interchanges between syn and anti conformations. The syn conformation is more frequently present in the trajectory, which agrees with the recent results [30]. Conformation about the glycosidic angle does not correspond to the specific conformation of the methionine moiety as it is a flexible part of the molecule.…”

Section: Resultssupporting

confidence: 90%

“…As a result, we obtained 39 interproton distances of SAM with respective error values. Previous studies examined mostly the conformation of the ribose and its spatial relationship with adenine and reported no more than 14 distances [29, 30]. Our data provide a high resolution input for the calculations aimed at conformation prediction, including information of the relative position between all of the moieties of SAM (Table 1), which was not available before.…”

Section: Resultsmentioning

confidence: 94%

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Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites

Perlinska

Stasiulewicz

Nawrocka

et al. 2019

Preprint

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S-adenosylmethionine (SAM) is one of the most important enzyme substrates. It is vital for the function of various proteins, including large group of methyltransferases (MTs). Intriguingly, some bacterial and eukaryotic MTs, while catalysing the same reaction, possess significantly different topologies, with the former being a knotted one. Here, we conducted a comprehensive analysis of SAM conformational space and factors that affect its vastness. We investigated SAM in two forms: free in water (via NMR studies and explicit solvent simulations) and bound to proteins (based on all data available in the PDB). We identified structural descriptors -angles which show the major differences in SAM conformation between unknotted and knotted methyltransferases. Moreover, we report that this is caused mainly by a characteristic for knotted MTs tight binding site formed by the knot and the presence of adenine-binding loop. Additionally, we elucidate conformational restrictions imposed on SAM molecules by other protein groups in comparison to conformational space in water. Author summaryThe topology of a folded polypeptide chain has great impact on the resulting protein function and its interaction with ligands. Interestingly, topological constraints appear to affect binding of one of the most ubiquitous substrates in the cell, S-adenosylmethionine (SAM), to its target proteins. Here, we demonstrate how binding sites of specific proteins restrict SAM conformational freedom in comparison to its unbound state, with a special interest in proteins with non-trivial topology, including an exciting group of knotted methyltransferases. Using a vast array of computational methods combined with NMR experiments, we identify key structural features of knotted methyltransferases that impose unorthodox SAM conformations. We compare them with the characteristics of standard, unknotted SAM binding proteins. These results are significant for understanding differences between analogous, yet topologically different enzymes, as well as for future rational drug design. October 7, 2019 1/22 1 S-adenosylmethionine (SAM or AdoMet) is an ubiquitous molecule and the second most 2 widely used enzyme substrate after ATP [1]. It is utilized in many different chemical 3 reactions, including transfer of the methyl group. It acts as methyl donor for a variety 4 of methyltransferases (MTs), involved in methylation of small molecules [2], proteins [3], 5 DNA [4], and RNA [5]. Interestingly, SAM binds not only to proteins but also to RNA -6 it is a substrate for riboswitches [6]. 7The diversity of molecules capable of binding SAM is great not only in a variety of 8 performed functions, but also in their structure and topology. In the case of 9 SAM-dependent methyltransferases, the proteins are divided into five classes, each with 10 a different fold, including a knotted one [7]. The set of knotted methyltransferases 11 (MTs) is the largest group of all known knotted proteins, which structures comprise now 12 about 2% of PDB's deposits. Interestingly, all of t...

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Section: Resultssupporting

confidence: 90%

Section: Resultsmentioning

confidence: 94%

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites

Perlinska

Stasiulewicz

Nawrocka

et al. 2019

Preprint

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“…Although time‐consuming, it may be possible to accurately determine the 3D structure of a molecule with these data. [ 110 ] One major limitation is the need for a well‐resolved 1 H spectrum, something that is relatively uncommon in complex natural product NMR spectra.…”

Section: Determining Stereochemistry Can Be Particularly Trickymentioning

confidence: 99%

Minimizing the risk of deducing wrong natural product structures from NMR data

Burns

Reynolds

2019

Magnetic Reson in Chemistry

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There continues to be a disturbing number of natural products reported in the literature whose structures are incorrect. At least in part, this reflects the fact that many natural product chemists have limited formal nuclear magnetic resonance training. Gaps in training and lack of awareness regarding the challenges and ambiguities associated with two‐dimensional nuclear magnetic resonance data interpretation can easily lead to errors in structure elucidation. The purpose of this tutorial is to point out some of these issues, highlight the kinds of errors that have been made and provide specific advice on how to avoid these missteps such that the risk of reporting a wrong structure is minimized.

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“…The force field parameters for SAM are based on electrostatic reparametrized force field parameters from Saez and Vöhringer-Martinez 49 as described and tested previously. 50 The parameters for the 4Fe4S cluster are based on a recent parametrisation of biological relevant iron-sulfur clusters by Carvalho and Swart. 51 These parameters showed good structural identity of the clusters as shown in the MD analysis in Section 1.4 of the Supporting Information.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Radical Stabilization Energies for Enzyme Engineering – Tackling the Substrate Scope of the Radical Enzyme QueE

Suess¹,

Martins²,

Croft³

et al. 2019

Preprint

Self Cite

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Experimental assessment of the reaction mechanisms and profiles of radical enzymes can be severely challenging due to the reactive nature of the intermediates, and sensitivity of cofactors such as iron sulfur clusters. Here we present an enzyme-directed computational methodology for the assessment of thermodynamic reaction profiles and screening for radical stabilization energies (RSEs) for the assessment of catalytic turnovers in radical enzymes. We have applied this new screening method to the radical SAM enzyme CPH4 synthase (QueE), following a detailed molecular dynamics (MD) analysis that clarifies the role of both specific enzyme residues and bound Mg2+, Ca2+ or Na+. The MD simulations provided the basis for a statistical approach to sample different conformational outcomes. RSE calculation at the M06-2X/6-31+G* level of theory provided the most computationally cost-effective assessment of enzyme-based energies, facilitated by an initial triage using semi-empirical methods. The impact of intermolecular interactions on RSE was clearly established and application to the assessment of potential alternative substrates (focusing on radical clock type rearrangements) proposes a selection of carbon-substituted analogues that would react to afford cyclopropylcarbinyl radical intermediates, as candidates for catalytic turnover by QueE.

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Improved NOE fitting for flexible molecules based on molecular mechanics data – a case study with S-adenosylmethionine

Cited by 28 publications

References 60 publications

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites

Minimizing the risk of deducing wrong natural product structures from NMR data

Radical Stabilization Energies for Enzyme Engineering – Tackling the Substrate Scope of the Radical Enzyme QueE

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