Analyses of protein cores reveal fundamental differences between solution and crystal structures

Mei, Zhe; Treado, John D.; Grigas, Alex T.; Levine, Zachary A.; Regan, Lynne; O’Hern, Corey S.

doi:10.1002/prot.25884

Cited by 19 publications

(31 citation statements)

References 23 publications

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“…In X-ray crystallographic structures, protein residues may be, for example, more densely packed than they are in a solution [32]. In the X-ray crystal structure of P450-TT (see Methods), the distance between Gln66 and Arg88 is~5.91 Å and these residues' surface figures (Figures 5 and 6) shows that the substrate channel is tightly closed.…”

Section: Resultsmentioning

confidence: 99%

Molecular Dynamics Simulations of a Cytochrome P450 from Tepidiphilus thermophilus (P450-TT) Reveal How Its Substrate-Binding Channel Opens

et al. 2021

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Cytochrome P450s (P450) are important enzymes in biology with useful biochemical reactions in, for instance, drug and xenobiotics metabolisms, biotechnology, and health. Recently, the crystal structure of a new member of the CYP116B family has been resolved. This enzyme is a cytochrome P450 (CYP116B46) from Tepidiphilus thermophilus (P450-TT) and has potential for the oxy-functionalization of organic molecules such as fatty acids, terpenes, steroids, and statins. However, it was thought that the opening to its hitherto identified substrate channel was too small to allow organic molecules to enter. To investigate this, we performed molecular dynamics simulations on the enzyme. The results suggest that the crystal structure is not relaxed, possibly due to crystal packing effects, and that its tunnel structure is constrained. In addition, the simulations revealed two key amino acid residues at the mouth of the channel; a glutamyl and an arginyl. The glutamyl’s side chain tightens and relaxes the opening to the channel in conjunction with the arginyl’s, though the latter’s side chain is less dramatically changed after the initial relaxation of its conformations. Additionally, it was observed that the effect of increased temperature did not considerably affect the dynamics of the enzyme fold, including the relative solvent accessibility of the amino acid residues that make up the substrate channel wall even as compared to the changes that occurred at room temperature. Interestingly, the substrate channel became distinguishable as a prominent tunnel that is likely to accommodate small- to medium-sized organic molecules for bioconversions. That is, P450-TT has the ability to pass appropriate organic substrates to its active site through its elaborate substrate channel, and notably, is able to control or gate any molecules at the opening to this channel.

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Section: Resultsmentioning

confidence: 99%

Molecular Dynamics Simulations of a Cytochrome P450 from Tepidiphilus thermophilus (P450-TT) Reveal How Its Substrate-Binding Channel Opens

et al. 2021

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“…In addition to the packing-generation protocol described in Sec. II, we employ the protocol [58] with thermal fluctuations described in Appendix C. As in 2D, we find that φ J increases with T , as shown in Fig. 13.…”

Section: Appendix Dmentioning

confidence: 74%

“…We repeat this thermalization, compression, and energy min- imization process until reaching jamming onset with a pressure that satisfies 10 −7 < P < 2 × 10 −7 when the system is in force balance. (A similar protocol has been implemented to generate jammed packings of 3D rigid bumpy particles [58].) We studied a range of temperatures from T = 10 −6 to 10 −2 .…”

Section: Appendix Cmentioning

confidence: 99%

The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions

Wang¹,

Treado²,

Boromand³

et al. 2021

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We investigate the structural, vibrational, and mechanical properties of jammed packings of deformable particles with shape degrees of freedom in three dimensions (3D). Each 3D deformable particle is modeled as a surface-triangulated polyhedron, with spherical vertices whose positions are determined by a shape-energy function with terms that constrain the particle surface area, volume, and curvature, and prevent interparticle overlap. We show that jammed packings of deformable particles without bending energy possess low-frequency, quartic vibrational modes, whose number decreases with increasing asphericity and matches the number of missing contacts relative to the isostatic value. In contrast, jammed packings of deformable particles with non-zero bending energy are isostatic in 3D, with no quartic modes. We find that the contributions to the eigenmodes of the dynamical matrix from the shape degrees of freedom are significant over the full range of frequency and shape parameters for particles with zero bending energy. We further show that the ensembleaveraged shear modulus G scales with pressure P as G ∼ P β , with β ≈ 0.75 for jammed packings of deformable particles with zero bending energy. In contrast, β ≈ 0.5 for packings of deformable particles with non-zero bending energy, which matches the value for jammed packings of soft, spherical particles with fixed shape. These studies underscore the importance of incorporating particle deformability and shape change when modeling the properties of jammed soft materials.

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“…For example, molecular dynamics (MD) simulations are often used to analyze thermal fluctuations in folded proteins. To what extent do the protein conformations sampled in such MD simulations recapitulate the packing properties of experimentally observed protein structures 66 ? The model developed here can be used in concert with MD simulations to filter out unphysical conformations, which will have low values of GDT, without using knowledge of the experimentally observed protein structure.…”

Section: Discussionmentioning

confidence: 99%

“…To estimate an average error, the predicted scores were normalized so that they fall within 0 to 1. The AUC values were averaged over GDT cutoffs from 40 66 ? The model developed here can be used in concert with MD simulations to filter out unphysical conformations, which will have low values of GDT, without using knowledge of the experimentally observed protein structure.…”

Section: Discussionmentioning

confidence: 99%

Using physical features of protein core packing to distinguish real proteins from decoys

et al. 2020

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The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute significantly to their stability. We used two sources to obtain datasets of decoys to compare with real protein structures: submissions to the biennial Critical Assessment of protein Structure Prediction competition, in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence, and also decoys generated by 3DRobot, which have user‐specified global root‐mean‐squared deviations from experimentally determined structures. Our analysis revealed that both sets of decoys possess cores that do not recapitulate the key features that define real protein cores. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a feed‐forward neural network, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoy structures with similar accuracy to that obtained by state‐of‐the‐art methods that incorporate many additional features. The small number of physical features makes our model interpretable, emphasizing the importance of protein packing and hydrophobicity in protein structure prediction.

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Analyses of protein cores reveal fundamental differences between solution and crystal structures

Cited by 19 publications

References 23 publications

Molecular Dynamics Simulations of a Cytochrome P450 from Tepidiphilus thermophilus (P450-TT) Reveal How Its Substrate-Binding Channel Opens

Molecular Dynamics Simulations of a Cytochrome P450 from Tepidiphilus thermophilus (P450-TT) Reveal How Its Substrate-Binding Channel Opens

The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions

Using physical features of protein core packing to distinguish real proteins from decoys

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