On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

Sucrose and Gibberellic Acid Binding Stabilize the Inward-Open Conformation of AtSWEET13: A Molecular Dynamics Study

In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key growth hormone. However, the dynamic mechanisms underlying sucrose and GA3 binding and transport remain elusive. Here, we employed microsecond-scale molecular dynamics (MD) simulations to investigate the influence of sucrose and GA3 binding on SWEET13 transporter motions. While sucrose exhibits high flexibility within the binding pocket, GA3 remains firmly anchored in the central cavity. Binding of both ligands increases the average channel radius along the transporter's principal axis. In contrast to the apo form, which retains its initial conformation throughout the simulation, ligand-bound complexes undergo a significant conformational transition characterized by further opening of the intracellular gate relative to the inward-open crystal structure (5XPD). This opening is driven by ligand-induced bending of helix V, stabilizing the inward-open state. Sucrose binding notably enhances the flexibility of the intracellular gate and amplifies anticorrelated motions between the N- and C-terminal domains at the intracellular side, suggesting an opening-closing motion of these domains. Principal component analysis revealed that this gating motion is most pronounced in the sucrose complex and minimal in the apo form, highlighting sucrose's ability to induce high-amplitude gating. Our binding free energy calculations indicate that SWEET13 has lower binding affinity for sucrose compared to GA3, consistent with its role in sugar transport. These results provide insight into key residues involved in sucrose and GA3 binding and transport, advancing our understanding of SWEET13 dynamics.

Exploring cotton plant compounds for novel treatments against brain-eating Naegleria fowleri: An In-silico approach

To find potential inhibitors of Naegleria fowleri S-adenosyl-L-homocysteine hydrolase (NfSAHH), a brain-eating parasite, structure-based drug design was adopted. N. fowlerica causes primary amebic meningoencephalitis (PAM), a fatal central nervous system (CNS) disorder if untreated. NfSAHH protein (PDB ID: 5v96), involved in parasite growth and gene regulation, was targeted and screened against 163 metabolites from Gossypium hirsutum (cotton plant). With the aid of different software and web tools, the metabolites were subjected to several analyses. The RMSD was evaluated to validate our molecular docking strategy. Neplanocin A, a common anti-parasitic medication, was used as a reference to select top ligands for post-docking studies. Significant interactions were observed with residues THR-198, HIS-395, and MET-400. The drug-likeness of the top fifty hits was analyzed using Lipinski, Ghose, Veber, Egan, and Muegge rules. The top ten compounds following Lipinski's RO5 were studied regarding medicinal chemistry, pharmacokinetic simulation, and Swiss target prediction. Advanced strategies, including molecular dynamic simulations, binding energy calculations, and principal component analysis, were employed for the top three hits, namely curcumin, heliocide H2, and piceid, which indicated that heliocide H2 is the most promising candidate, while curcumin and piceid may need further optimization to improve their stability. Overall, the top ten phytochemicals, dotriacontanol, melissic acid, curcumin, 6,6'-dimethoxygossypol, phytosphingosine 2, methyl stearate, stearic acid, piceid, heliocide H2, and 6-methoxygossypol, reported in our study, are worthy enough to be subjected to in vivo and in vitro experimentation to find a novel drug to treat PAM.

Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants

The severe acute respiratory syndrome (SARS) coronavirus 2 (CoV-2) variant Omicron spread more rapid than the other variants of SARS-CoV-2 virus. Mutations on the Spike (S) protein receptor-binding domain (RBD) are critical for the antibody resistance and infectivity of the SARS-CoV-2 variants. In this study, we have used accelerated molecular dynamics (aMD) simulations and free energy calculations to present a systematic analysis of the affinity and conformational dynamics along with the interactions that drive the binding between Spike protein RBD and human angiotensin-converting enzyme 2 (ACE2) receptor. We evaluate the impacts of the key mutation that occur in the RBDs Omicron and other variants in the binding with the human ACE2 receptor. The results show that S protein Omicron has stronger binding to the ACE2 than other variants. The evaluation of the decomposition energy per residue shows the mutations N440K, T478K, Q493R and Q498R observed in Spike protein of SARS-CoV-2 provided a stabilization effect for the interaction between the SARS-CoV-2 RBD and ACE2. Overall, the results demonstrate that faster spreading of SARS-CoV-2 Omicron may be correlated with binding affinity of S protein RBD to ACE2 and mutations of uncharged residues to positively charged residues such as Lys and Arg in key positions in the RBD.

Assessment of the PETase conformational changes induced by poly(ethylene terephthalate) binding

Recently, a bacterium strain of Ideonella sakaiensis was identified with the uncommon ability to degrade the poly(ethylene terephthalate) (PET). The PETase from I. sakaiensis strain 201-F6 (IsPETase) catalyzes the hydrolysis of PET converting it to mono(2-hydroxyethyl) terephthalic acid (MHET), bis(2-hydroxyethyl)-TPA (BHET), and terephthalic acid (TPA). Despite the potential of this enzyme for mitigation or elimination of environmental contaminants, one of the limitations of the use of IsPETase for PET degradation is the fact that it acts only at moderate temperature due to its low thermal stability. Besides, molecular details of the main interactions of PET in the active site of IsPETase remain unclear. Herein, molecular docking and molecular dynamics (MD) simulations were applied to analyze structural changes of IsPETase induced by PET binding. Results from the essential dynamics revealed that the β1-β2 connecting loop is very flexible. This loop is located far from the active site of IsPETase and we suggest that it can be considered for mutagenesis to increase the thermal stability of IsPETase. The free energy landscape (FEL) demonstrates that the main change in the transition between the unbound to the bound state is associated with the β7-α5 connecting loop, where the catalytic residue Asp206 is located. Overall, the present study provides insights into the molecular binding mechanism of PET into the IsPETase structure and a computational strategy for mapping flexible regions of this enzyme, which can be useful for the engineering of more efficient enzymes for recycling plastic polymers using biological systems.

A new analogue of islet neogenesis associated protein with higher structural and plasma stability

Islet Neogenesis Associated Protein pentadecapeptide (INGAP-PP) increases β-cell mass and function in experimental animals. A short clinical trial also yielded promising results. However, HTD4010, a new peptide derived from INGAP-PP, was developed in order to optimize its specific effects by minimizing its side effects. To study and compare the tertiary structure, stability dynamics, and plasma stability of HTD4010, an INGAP-PP analogue. Both peptides were pre-incubated in human, rat and mouse plasma at 37 °C, and their presence was identified and quantified by high performance liquid chromatography at different time-points. GROMACS 2019 package and the Gromos 54A7 force field were used to evaluate overall correlated motion of the peptide molecule during molecular dynamics simulation by essential dynamics. HTD4010 exhibited significantly larger plasma stability than INGAP-PP, and its structural stability was almost 3.36-fold higher than INGAP-PP. These results suggest that HTD4010 may facilitate longer tissue interaction, thereby developing higher potential biological effects. If so, HTD4010 may become a promising therapeutic agent to treat people with diabetes. Communicated by Ramaswamy H. Sarma.

Dynamics fingerprints of active conformers of epidermal growth factor receptor kinase

Epidermal growth factor receptor (EGFR) is a prototypical cell-surface receptor that plays a key role in the regulation of cellular signaling, proliferation and differentiation. Mutations of its kinase domain have been associated with the development of a variety of cancers and, therefore, it has been the target of drug design. Single amino acid substitutions (SASs) in this domain have been proven to alter the equilibrium of pre-existing conformer populations. Despite the advances in structural descriptions of its so-called active and inactive conformations, the associated dynamics aspects that characterize them have not been thoroughly studied yet. As the dynamic behaviors and molecular motions of proteins are important for a complete understanding of their structure-function relationships we present a novel procedure, using (or based on) normal mode analysis, to identify the collective dynamics shared among different conformers in EGFR kinase. The method allows the comparison of patterns of low-frequency vibrational modes defining representative directions of motions. Our procedure is able to emphasize the main similarities and differences between the collective dynamics of different conformers. In the case of EGFR kinase, two representative directions of motions have been found as dynamics fingerprints of the active conformers. Protein motion along both directions reveals to have a significant impact on the cavity volume of the main pocket of the active site. Otherwise, the inactive conformers exhibit a more heterogeneous distribution of collective motions. © 2018 Wiley Periodicals, Inc.