Interactions of amyloid peptides with lipid membranes

The aggregation of amyloid proteins into fibrils is a hallmark of several diseases including Alzheimer’s (AD), Parkinson’s, and Type II diabetes. This aggregation process involves the formation of small size oligomers preceding the formation of insoluble fibrils. Recent studies have shown that these oligomers are more likely to be responsible for cell toxicity than fibrils. A possible mechanism of toxicity involves the interaction of oligomers with the cell membrane compromising its integrity. In particular, oligomers may form pore-like structures in the cell membrane affecting its permeability or they may induce lipid loss via a detergent-like effect. This dissertation aims to provide insights into these mechanisms of toxicity, which are poorly understood at the atomic level. This dissertation kicks off with a molecular dynamics study of the interaction of individual amyloid-like peptides with lipid bilayers. It is found that both electrostatic and hydrophobic interactions contribute to peptide-membrane binding. In particular, the attraction of peptide to lipid bilayer is dominated by electrostatic interactions and hydrophobicity drives the burial of non-polar side chains into the interior of the bilayer. By changing the peptide sequence, positive net charges are shown to significantly strengthen peptide-membrane binding, whereas negative charges reduce their affinity drastically. Moreover, peptide-membrane binding can also be regulated by the position of positive residues in the peptide sequence which alters the exposure of positive side chains to the solvent. These results provide insights into the mechanism accounting for cell toxicity of amyloid proteins and the designing of antimicrobial peptides. In this study, the first all-atom simulations are performed in which membrane-bound amphipathic peptides self-assemble into β-sheets that subsequently either form stable pores inside the bilayer or drag lipids out of the membrane surface. An analysis of these simulations shows that the acyl tails of lipids interact strongly with non-polar side chains of peptides deposited on the membrane. These strong interactions enable lipids to be dragged out of the bilayer by oligomeric structures accounting for detergent-like damage. Moreover, they disturb the orientation of lipid tails that are close to peptides. These distortions in lipid orientation are reduced close to pores contributing to stabilize these structures. These simulations also show that naturally twisted β-sheets are intermediate structures on pathway to poration. They enable water to partially penetrate the membrane triggering β-sheets to tilt and penetrate the membrane. The latter reduces interactions of solvent molecules with non-polar moieties of lipids. In addition, our simulations show that fibril-like structures produce little damage to lipid membranes as non-polar side chains in these structures are unavailable to interact with the acyl tail of lipids

Visualization of intermediate representations in Neural Machine Translation

The intention of this research is to find a way to visualize the result of Neural Machine Translation got from the encoder. Present the result in an intermediate web page to make it easy to be comprehended

Demonstration of a Novel HIV-1 Restriction Phenotype from a Human T Cell Line

Although retroviruses may invade host cells, a productive infection can be established only after the virus counteracts inhibition from different types of host restriction factors. Fv1, APOBEC3G/F, TRIM5alpha, ZAP, and CD317 inhibit the replication of different retroviruses by interfering with viral uncoating, reverse transcription, nuclear import, RNA stability, and release. In humans, although APOBEC3G/3F and CD317 block HIV-1 replication, their antiviral activities are neutralized by viral proteins Vif and Vpu. So far, no human gene has been found to effectively block wild type HIV-1 replication under natural condition. Thus, identification of such a gene product would be of great medical importance for the development of HIV therapies.In this study, we discovered a new type of host restriction against the wild type HIV-1 from a CD4/CXCR4 double-positive human T cell line. We identified a CEM-derived cell line (CEM.NKR) that is highly resistant to productive HIV-1 infection. Viral production was reduced by at least 1000-fold when compared to the other permissive human T cell lines such as H9, A3.01, and CEM-T4. Importantly, this resistance was evident at extremely high multiplicity of infection. Further analyses demonstrated that HIV-1 could finish the first round of replication in CEM.NKR cells, but the released virions were poorly infectious. These virions could enter the target cells, but failed to initiate reverse transcription. Notably, this restriction phenotype was also present in CEM.NKR and 293T heterokaryons.These results clearly indicate that CEM.NKR cells express a HIV inhibitory gene(s). Further characterization of this novel gene product(s) will reveal a new antiretroviral mechanism that directly inactivates wild type HIV-1

APOBEC3G and APOBEC3F Require an Endogenous Cofactor to Block HIV-1 Replication

APOBEC3G (A3G)/APOBEC3F (A3F) are two members of APOBEC3 cytidine deaminase subfamily. Although they potently inhibit the replication of vif-deficient HIV-1, this mechanism is still poorly understood. Initially, A3G/A3F were thought to catalyze C-to-U transitions on the minus-strand viral cDNAs during reverse transcription to disrupt the viral life cycle. Recently, it was found more likely that A3G/A3F directly interrupts viral reverse transcription or integration. In addition, A3G/A3F are both found in the high-molecular-mass complex in immortalized cell lines, where they interact with a number of different cellular proteins. However, there has been no evidence to prove that these interactions are required for A3G/A3F function. Here, we studied A3G/A3F-restricted HIV-1 replication in six different human T cell lines by infecting them with wild-type or vif-deficient HIV-1. Interestingly, in a CEM-derived cell line CEM-T4, which expresses high levels of A3G/A3F proteins, the vif-deficient virus replicated as equally well as the wild-type virus, suggesting that these endogenous antiretroviral genes lost anti-HIV activities. It was confirmed that these A3G/A3F genes do not contain any mutation and are functionally normal. Consistently, overexpression of exogenous A3G/A3F in CEM-T4 cells still failed to restore their anti-HIV activities. However, this activity could be restored if CEM-T4 cells were fused to 293T cells to form heterokaryons. These results demonstrate that CEM-T4 cells lack a cellular cofactor, which is critical for A3G/A3F anti-HIV activity. We propose that a further study of this novel factor will provide another strategy for a complete understanding of the A3G/A3F antiretroviral mechanism

Visualization of intermediate representations in Neural Machine Translation

The intention of this research is to find a way to visualize the result of Neural Machine Translation got from the encoder. Present the result in an intermediate web page to make it easy to be comprehended