Identification of functionally key residues in maltose transporter with an elastic network model-based thermodynamic method

<p>Periplasmic binding protein-dependent maltose transport system (MBP-MalFGK₂) of <i>Escherichia coli</i>, an important member of the Adenosine triphosphate-binding cassette transporter superfamily, is in charge of the transportation of maltoses across cellular membrane. Studies have shown that this transport processes are activated by the binding of maltose and are accompanied by large-scale cooperative movements between different domains which are mediated by a network of important residues related to signal transduction and allosteric regulation. In this paper, the functionally crucial residues and long-range allosteric pathway of the regulation of the system by substrate were identified by utilising a coarse-grained thermodynamic method proposed by our group. The residues whose perturbations markedly change the binding free energy between maltoses and MBP-MalFGK₂ were considered to be key residues. In result, the key residues in 62 clusters distributed in different subdomains were identified successfully, and the results from our calculation are highly consistent with experimental and theoretical observations. Furthermore, we explored the long-range cooperation within the transporter. These studies will help us better understand the physical mechanism of the effects of the maltose on MBP-MalFGK₂ by long-range allosteric modulation.</p> <p></p

A Peptide-Coated Gold Nanocluster Exhibits Unique Behavior in Protein Activity Inhibition

Gold nanoclusters (AuNCs) can be primed for biomedical applications through functionalization with peptide coatings. Often anchored by thiol groups, such peptide coronae not only serve as passivators but can also endow AuNCs with additional bioactive properties. In this work, we use molecular dynamics simulations to study the structure of a tridecapeptide-coated Au₂₅ cluster and its subsequent interactions with the enzyme thioredoxin reductase 1, TrxR1. We find that, in isolation, both the distribution and conformation of the coating peptides fluctuate considerably. When the coated AuNC is placed around TrxR1, however, the motion of the highly charged peptide coating (+5e/peptide) is quickly biased by electrostatic attraction to the protein; the asymmetric coating acts to guide the nanocluster’s diffusion toward the enzyme’s negatively charged active site. After the AuNC comes into contact with TrxR1, its peptide corona spreads over the protein surface to facilitate stable binding with protein. Though individual salt bridge interactions between the tridecapeptides and TrxR1 are transient in nature, the cooperative binding of the peptide-coated AuNC is very stable, overall. Interestingly, the biased corona peptide motion, the spreading and the cooperation between peptide extensions observed in AuNC binding are reminiscent of bacterial stimulus-driven approaching and adhesion mechanisms mediated by cilia. The prevailing AuNC binding mode we characterize also satisfies a notable hydrophobic interaction seen in the association of thioredoxin to TrxR1, providing a possible explanation for the AuNC binding specificity observed in experiments. Our simulations thus suggest this peptide-coated AuNC serves as an adept thioredoxin mimic that extends an array of auxiliary structural components capable of enhancing interactions with the target protein in question

The first slowest motion modes of NpAS (A) and DgAS (B) revealed by the ANM.

<p>The length of the cone in each C_α atom represents the magnitude of movement and its direction indicates the moving direction.</p

Insight into the Structure, Dynamics and the Unfolding Property of Amylosucrases: Implications of Rational Engineering on Thermostability

<div><p>Amylosucrase (AS) is a kind of glucosyltransferases (E.C. 2.4.1.4) belonging to the Glycoside Hydrolase (GH) Family 13. In the presence of an activator polymer, in vitro, AS is able to catalyze the synthesis of an amylose-like polysaccharide composed of only α-1,4-linkages using sucrose as the only energy source. Unlike AS, other enzymes responsible for the synthesis of such amylose-like polymers require the addition of expensive nucleotide-activated sugars. These properties make AS an interesting enzyme for industrial applications. In this work, the structures and topology of the two AS were thoroughly investigated for the sake of explaining the reason why <em>Deinococcus geothermalis</em> amylosucrase (DgAS) is more stable than <em>Neisseria polysaccharea</em> amylosucrase (NpAS). Based on our results, there are two main factors that contribute to the superior thermostability of DgAS. On the one hand, DgAS holds some good structural features that may make positive contributions to the thermostability. On the other hand, the contacts among residues of DgAS are thought to be topologically more compact than those of NpAS. Furthermore, the dynamics and unfolding properties of the two AS were also explored by the gauss network model (GNM) and the anisotropic network model (ANM). According to the results of GNM and ANM, we have found that the two AS could exhibit a shear-like motion, which is probably associated with their functions. What is more, with the discovery of the unfolding pathway of the two AS, we can focus on the weak regions, and hence designing more appropriate mutations for the sake of thermostability engineering. Taking the results on structure, dynamics and unfolding properties of the two AS into consideration, we have predicted some novel mutants whose thermostability is possibly elevated, and hopefully these discoveries can be used as guides for our future work on rational design.</p> </div

The distribution of proline residues among each domain.

<p>The distribution of proline residues among each domain.</p

The unfolding curves for each domains of NpAS and DgAS.

<p>Here, the unfolding curves for the intra domain contacts of NpAS and DgAS are displayed in (A) and (B), and those for the inter domain contacts of NpAS and DgAS are shown in (C) and (D), respectively.</p

The Number of Contact per Residue (NCPR) for each domain of NpAS and DgAS.

<p>The Number of Contact per Residue (NCPR) for each domain of NpAS and DgAS.</p

Estimated folding free energies (kcal·mol⁻¹) for NpAS and DgAS.

a<p>H-bond energy for the backbone-backbone type.</p>b<p>H-bond energy for the sidechain-backbone and sidechain-backbone type.</p>c<p>Electrostatics energy contributions of the charged pairs.</p>d<p>Energy contribution by conformational entropy at room temperature.</p>e<p>Helix dipole (mainly) and others.</p

The contact maps for the native (A), LNNC = 100 (B), 200 (C) and 500 (C) states of DgAS (D).

<p>Each contact is represented by a “+” mark.</p

Virtual ala-scan for the seven additional glycine residues of DgAS.

<p>Virtual ala-scan for the seven additional glycine residues of DgAS.</p