The simplest molecule with a disulfide bond, hydrogen disulfide (HSSH), represents an ideal test model for the determination of accurate gas-phase equilibrium structures for molecules containing ...third-row elements. First, pure theoretical composite schemes based on the coupled-cluster (CC) theory, which take into account the extrapolation to the complete basis set limit, core-valence correlation contributions, higher excitations in the CC expansion, and relativistic effects, allow for calculating accurate reference geometrical parameters. Second, using experimental vibrational ground-state rotational constants for a set of isotopologues, in conjunction with vibrational corrections based on second-order vibrational perturbation theory formulation and the recently developed Molecular Structure Refinement (MSR) software, we have determined the semi-experimental (SE) equilibrium structure of HSSH. The comparison of SE parameters with the computational best estimates shows an agreement within 0.001 Å for distances and 0.1° for angles, thus further validating the SE approach as cost-effective, provided that the required experimental data are available. Together with the intrinsic interest of HSSH, also in connection with astrochemistry, highly accurate structural properties of a prototypical disulfide bond can serve as references for future studies of larger molecules of biological interest containing this challenging moiety.
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•Theoretical equilibrium structure from composite schemes.•Semi-experimental equilibrium structure.•Disulfide bond length determined with 1 mÅ accuracy.
Cyclobutane pyrimidine dimers (CpDs) are among the most common DNA lesions occurring due to the interaction with ultraviolet light. While photolyases have been well known as external factors ...repairing CpDs, the intrinsic self-repairing capabilities of the GATdouble bond, length as m-dashT DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order ADC(2) method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the Tdouble bond, length as m-dashT dimer. Consequently, the molecular mechanism of GATdouble bond, length as m-dashT self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S
potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S
/S
state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.
The HutP protein from B. subtilis regulates histidine metabolism by interacting with an antiterminator mRNA hairpin in response to the binding of l-histidine and Mg
. We studied the functional ...ligand-bound HutP hexamer complexed with two mRNAs using all-atom microsecond-scale explicit-solvent MD simulations performed with the Amber force fields. The experimentally observed protein-RNA interface exhibited good structural stability in the simulations with the exception of some fluctuations in an unusual adenine-threonine interaction involving two closely spaced H-bonds. We further investigated this interaction by comparing QM/MM and MM optimizations, using the QM region comprising almost 350 atoms described at the DFT-D3 level. The QM/MM method clearly improved the adenine-threonine interaction compared to MM, especially when the X-H bond lengths were frozen during the MM optimization to mimic the use of SHAKE in the MD simulations. Thus, both the MM approximation and the use of SHAKE can compromise the description of H-bonds at protein-RNA interfaces. The simulations also revealed a notable Mg
-parameter dependence in the behavior of the ligand-binding pocket (LBP). With the SPC/E water model, the 12-6 Åqvist and Li&Merz parameters provided an entirely stable LBP structure, but the 12-6 Allnér and 12-6-4 Li&Merz parametrizations resulted in a progressive loss of direct nitrogen-Mg
LBP coordination. The Allnér and Li&Merz 12-6 parametrizations were also tested with the TIP3P water model; the LBP was destabilized in both cases. This illustrates the difficulty of consistently describing different Mg
interactions using nonpolarizable force fields. Overall, the simulations support the hypothesis that HutP protein becomes fully structured upon ligand binding. Subsequent RNA binding does not affect the protein structure, in keeping with the mechanism inferred from experimental structures.
Phosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single nonbridging oxygen of the phosphate is replaced with a sulfur atom. PT can stabilize RNAs by protecting ...them from hydrolysis and is commonly used as a tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stability and electronic structure. Here, we present molecular dynamics (MD) simulations, quantum mechanical (QM) calculations, and NMR spectroscopy measurements, exploring the effects of PT modifications in the structural context of the neomycin-sensing riboswitch (NSR). The NSR is the smallest biologically functional riboswitch with a well-defined structure stabilized by a U-turn motif. Three of the signature interactions of the U-turn: an H-bond, an anion-π interaction, and a potassium binding site; are formed by RNA phosphates, making the NSR an ideal model for studying how PT affects RNA structure and dynamics. By comparing with high-level QM calculations, we reveal the distinct physical properties of the individual interactions facilitated by the PT. The sulfur substitution, besides weakening the direct H-bond interaction, reduces the directionality of H-bonding while increasing its dispersion and induction components. It also reduces the induction and increases the dispersion component of the anion-π stacking. The sulfur force-field parameters commonly employed in the literature do not reflect these distinctions, leading to the unsatisfactory description of PT in simulations of the NSR. We show that it is not possible to accurately describe the PT interactions using one universal set of van der Waals sulfur parameters and provide suggestions for improving the force-field performance.
Real‐space quantum‐based refinement for cryo‐EM: Q|R#3 Wang, Lum; Kruse, Holger; Sobolev, Oleg V. ...
Acta crystallographica. Section D, Structural biology,
December 2020, 2020-12-01, 20201201, Letnik:
76, Številka:
12
Journal Article
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Electron cryo‐microscopy (cryo‐EM) is rapidly becoming a major competitor to X‐ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent ...spectacular technological improvements have led to significantly higher resolution three‐dimensional reconstructions, the average quality of cryo‐EM maps is still at the low‐resolution end of the range compared with crystallography. A long‐standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here, it is demonstrated that including accurate model geometry restraints derived from ab initio quantum‐chemical calculations (HF‐D3/6‐31G) can improve the refinement of an example structure (chain A of PDB entry 3j63). The robustness of the procedure is tested for additional structures with up to 7000 atoms (PDB entry 3a5x and chain C of PDB entry 5fn5) using the less expensive semi‐empirical (GFN1‐xTB) model. The necessary algorithms enabling real‐space quantum refinement have been implemented in the latest version of qr.refine and are described here.
The implementation of quantum‐based real‐space refinement in qr.refine is described.
Three‐dimensional structure models refined using low‐resolution data from crystallographic or electron cryo‐microscopy experiments can benefit from high‐quality restraints derived from ...quantum‐chemical methods. However, nonperiodic atom‐centered quantum‐chemistry codes do not inherently account for nearest‐neighbor interactions of crystallographic symmetry‐related copies in a satisfactory way. Here, these nearest‐neighbor effects have been included in the model by expanding to a super‐cell and then truncating the super‐cell to only include residues from neighboring cells that are interacting with the asymmetric unit. In this way, the fragmentation approach can adequately and efficiently include nearest‐neighbor effects. It has previously been shown that a moderately sized X‐ray structure can be treated using quantum methods if a fragmentation approach is applied. In this study, a target protein (PDB entry 4gif) was partitioned into a number of large fragments. The use of large fragments (typically hundreds of atoms) is tractable when a GPU‐based package such as TeraChem is employed or cheaper (semi‐empirical) methods are used. The QM calculations were run at the HF‐D3/6‐31G level. The models refined using a recently developed semi‐empirical method (GFN2‐xTB) were compared and contrasted. To validate the refinement procedure for a non‐P1 structure, a standard set of crystallographic metrics were used. The robustness of the implementation is shown by refining 13 additional protein models across multiple space groups and a summary of the refinement metrics is presented.
The C‐terminal coiled‐coil domain of transient receptor potential channel TRPP3 in space group P321 (PDB entry 4gif) is re‐refined with restraints from quantum chemistry using Hartree–Fock theory.
Cyclobutane pyrimidine dimers (CpDs) are among the most common DNA lesions occurring due to the interaction with ultraviolet light. While photolyases have been well known as external factors ...repairing CpDs, the intrinsic self-repairing capabilities of the GAT&z.dbd;T DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order ADC(2) method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the T&z.dbd;T dimer. Consequently, the molecular mechanism of GAT&z.dbd;T self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S
1
potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S
1
/S
0
state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.
QM/MM simulations elucidate the self-repair mechanism of the cyclobutane pyrimidine dimer.
QM/MM simulations elucidate the self-repair mechanism of the cyclobutane pyrimidine dimer.
Cyclobutane pyrimidine dimers (CpDs) are among the most common DNA lesions occurring due to the interaction ...with ultraviolet light. While photolyases have been well known as external factors repairing CpDs, the intrinsic self-repairing capabilities of the GAT
Created by potrace 1.16, written by Peter Selinger 2001-2019
T DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order ADC(2) method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the T
Created by potrace 1.16, written by Peter Selinger 2001-2019
T dimer. Consequently, the molecular mechanism of GAT
Created by potrace 1.16, written by Peter Selinger 2001-2019
T self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S
1
potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S
1
/S
0
state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.
Current interest in lone‐pair⋅⋅⋅π (lp⋅⋅⋅π) interactions is gaining momentum in biochemistry and (supramolecular) chemistry. However, the physicochemical origin of the exceptionally short (ca. 2.8 Å) ...oxygen‐to‐nucleobase plane distances observed in prototypical Z‐DNA CpG steps remains unclear. High‐level quantum mechanical calculations, including SAPT2+3 interaction energy decompositions, demonstrate that lp⋅⋅⋅π contacts do not result from n→π* orbital overlaps but from weak dispersion and electrostatic interactions combined with stereochemical effects imposed by the locally strained structural context. They also suggest that the carbon van der Waals (vdW) radii, originally derived for sp3 carbons, should not be used for smaller sp2 carbons attached to electron‐withdrawing groups. Using a more adapted carbon vdW radius results in these lp⋅⋅⋅π contacts being no longer of the sub‐vdW type. These findings challenge the whole lp⋅⋅⋅π concept that refers to elusive orbital interactions that fail to explain short interatomic contact distances.
Short lp⋅⋅⋅π contacts in Z‐DNA steps result from a combination of compression effects induced by a highly strained structural context and an effective van der Waals (vdW) radius of a guanine sp2 carbon atom that is estimated to be much smaller than the standard 1.70 Å vdW radius of sp3 carbons generally used to assess the sub‐vdW character of these interactions.
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