Conformational changes associated with L16P and T118M mutations in the membrane-embedded PMP22 protein, consequential in CMT-1A

<p>Peripheral myelin protein 22 (PMP22) resides in the plasma membrane and is required for myelin formation in the peripheral nervous system. Excess PMP22 mutants accumulate in the endoplasmic reticulum (ER) resulting in the inherited neuropathies of Charcot–Marie–Tooth disease. However, there was no evidence of the structure of PMP22 or how mutations affect its folding. Therefore, in this study, we combined bioinformatics and homology modeling approaches to obtain three-dimensional native and mutated PMP22 models and its anchoring to a POPC membrane, submitted to .5-μs MD simulations, to determine how the L16P and T118M mutations affect the conformational behavior of PMP22. In addition, we investigated the ability of the native and mutated species to accumulate in the ER, via interaction with RER1, by combining protein–protein docking and MD simulations, taking the conformations that were most representative of the native and mutated PMP22 systems and RER1 conformations. Principal component analysis over MD simulations revealed that L16P and T118M mutations resulted in increased structural instability compared to the native form, which is consistent with previous experimental findings of increased structural fluctuations along a loop connecting transmembrane α-helix1 and α-helix2. Docking and MD simulations coupled with the MMGBSA approach allowed the identification that the binding interface for the PMP22-RER1 complex takes place through transmembrane α-helix1 and α-helix2, with higher effective binding free energy values between the mutated PMP22 systems and RER1 than for the native PMP22, mainly through van der Waals interactions.</p

A study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations

<div><p>The anti-apoptotic B-cell lymphoma 2 (Bcl-2) protein interacts with several proteins that regulate the apoptotic properties of cells. In this research, we conduct several all-atom molecular dynamics (MD) simulations under high-temperature unfolding conditions, from 400 to 800 K, for 25 ns. These simulations were performed using a model of an engineered Bcl-2 human protein (Bcl-2-Δ22Σ3), which lacks 22 C-terminal residues of the transmembrane domain. The aim of this study is to gain insight into the structural behavior of Bcl-2-Δ22Σ3 by mapping the conformational movements involved in Bcl-2 stability and its biological function. To build a Bcl-2-Δ22Σ3 three-dimensional model, the protein core was built by homology modeling and the flexible loop domain (FLD, residues 33-91) by <i>ab initio</i> methods. Further, the entire protein model was refined by MD simulations. Afterwards, the production MD simulations showed that the FLD at 400 and 500 K has several conformations reaching into the protein core, whereas at 600 K some of the alpha-helices were lost. At 800 K, the Bcl-2 core is destabilized suggesting a possible mechanism for protein unfolding, where the alpha helices 1 and 6 were the most stable, and a reduction in the number of hydrogen bonds initially occurs. In conclusion, the structural changes and the internal protein interactions suggest that the core and the FLD are crucial components of Bcl-2 in its function of regulate ng access to the recognition sites of kinases and caspases.</p></div

Antiviral activity against influenza A H1N1 swine viral strain by AVPs derived from HA1 subunit.

<p>It is expressed as % of cell protection against viral infection, measured by MTT assay. The upper line in each figure indicates the tested AVP. </p

Antiviral activity against influenza A H5N2 avian viral strain by AVPs derived from HA1 subunit.

<p>It is expressed as % of cell protection against viral infection, measured by MTT assay. The upper line in each figure indicates the tested AVP.</p

Interaction sites among AVPs derived of C-t of the HA1 subunit targeting influenza A HA (3LZG).

<p>A) Sites of interaction. B) An amplification of C3<b>LB-HA</b> interaction with the proximal domain of HA.</p

Antiviral activity against influenza A Puerto Rico/916/34 (H1N1) viral strain by AVPs derived from HA2 subunit.

<p>It is expressed as % of cell protection against viral infection, measured by MTT assay. The upper line in each figure indicates the tested AVP.</p

Heterodimerization of the <i>Entamoeba histolytica</i> EhCPADH virulence complex through molecular dynamics and protein–protein docking

<p>EhCPADH is a protein complex involved in the virulence of <i>Entamoeba histolytica</i>, the protozoan responsible for human amebiasis. It is formed by the EhCP112 cysteine protease and the EhADH adhesin. To explore the molecular basis of the complex formation, three-dimensional models were built for both proteins and molecular dynamics simulations (MDS) and docking calculations were performed. Results predicted that the pEhCP112 proenzyme and the mEhCP112 mature enzyme were globular and peripheral membrane proteins. Interestingly, in pEhCP112, the propeptide appeared hiding the catalytic site (C167, H329, N348); while in mEhCP112, this site was exposed and its residues were found structurally closer than in pEhCP112. EhADH emerged as an extended peripheral membrane protein with high fluctuation in Bro1 and V shape domains. 500 ns-long MDS and protein–protein docking predictions evidenced different heterodimeric complexes with the lowest free energy. pEhCP112 interacted with EhADH by the propeptide and C-terminal regions and mEhCP112 by the C-terminal through hydrogen bonds. In contrast, EhADH bound to mEhCP112 by 442–479 residues, adjacent to the target cell-adherence region (480–600 residues), and by the Bro1 domain (9–349 residues). Calculations of the effective binding free energy and per residue free energy decomposition showed that EhADH binds to mEhCP112 with a higher binding energy than to pEhCP112, mainly through van der Waals interactions and the nonpolar part of solvation energy. The EhADH and EhCP112 structural relationship was validated in trophozoites by immunofluorescence, TEM, and immunoprecipitation assays. Experimental findings fair agreed with <i>in silico</i> results.</p

Bound and unbound fractions of <i>C2</i> in rat plasma and its blood-plasma partition ratio.

<p>Bound and unbound fractions of <i>C2</i> in rat plasma and its blood-plasma partition ratio.</p

Plasma pharmacokinetic parameters of <i>C2</i> determined by a non-compartmental model analysis after a single intravenous, oral, and intraperitoneal administration to Wistar rats at a doses of 50, 75 and 100 mg/kg.

<p>Values are presented the as the mean ± SD.</p

Pharmacokinetics in Wistar Rats of 5-[(4-Carboxybutanoyl)Amino]-2-Hydroxybenzoic Acid: A Novel Synthetic Derivative of 5-Aminosalicylic Acid (5-ASA) with Possible Anti-Inflammatory Activity - Fig 2

<p>(A) Biological matrix (plasma) chromatogram. (B) Chromatogram of 1 μg/mL <i>C2</i> standard. (C) Chromatogram of biological matrix spiked with ketamine, xylazine and heparin (D) Chromatogram of an <i>in vivo</i> plasma sample from a rat that had been administered <i>C2</i>.</p