Leveraging Bidirectional Nature of Allostery To Inhibit Protein-Protein Interactions (PPIs): A Case Study of PCSK9-LDLR Interaction.

The protein PCSK9 (proprotein convertase subtilisin/Kexin type 9) negatively regulates the recycling of LDLR (low-density lipoprotein receptor), leading to an elevated plasma level of LDL. Inhibition of PCSK9-LDLR interaction has emerged as a promising therapeutic strategy to manage hypercholesterolemia. However, the large interaction surface area between PCSK9 and LDLR makes it challenging to identify a small molecule competitive inhibitor. An alternative strategy would be to identify distal cryptic sites as targets for allosteric inhibitors that can remotely modulate PCSK9-LDLR interaction. Using several microseconds long molecular dynamics (MD) simulations, we demonstrate that on binding with LDLR, there is a significant conformational change (population shift) in a distal loop (residues 211-222) region of PCSK9. Consistent with the bidirectional nature of allostery, we establish a clear correlation between the loop conformation and the binding affinity with LDLR. Using a thermodynamic argument, we establish that the loop conformations predominantly present in the apo state of PCSK9 would have lower LDLR binding affinity, and they would be potential targets for designing allosteric inhibitors. We elucidate the molecular origin of the allosteric coupling between this loop and the LDLR binding interface in terms of the population shift in a set of salt bridges and hydrogen bonds. Overall, our work provides a general strategy toward identifying allosteric hotspots: compare the conformational ensemble of the receptor between the apo and bound states of the protein and identify distal conformational changes, if any. The inhibitors should be designed to bind and stabilize the apo-specific conformations.

Efficient light harvesting in self-assembled organic luminescent nanotubes.

Luminescent organic nanotubes derived from the co-assembly of cyanostilbene (CS) based cationic supramolecular polymers and bio-polyanion heparin, a known anticoagulant, have been utilized as highly efficient FRET (fluorescence resonance energy transfer) donors in aqueous media resulting in amplified acceptor emission in the orange-red and near-infrared (NIR). Energy transfer efficiencies higher than 80% and an ultra-high antenna effect of 150 were achieved even at high donor/acceptor ratios (500 : 1-100 : 1) translating to emission quenching of several hundred donors by one acceptor. Utilizing the temperature responsiveness of the FRET process, these systems were employed as ratiometric emission thermometers in the temperature range 20-90 °C. Moreover, the energy transfer was very effective in solid and polymer films. This allowed us to generate multi-color emissions ranging from blue to red including white light in solution as well as in solid and polymer films.

Traceless cysteine-linchpin enables precision engineering of lysine in native proteins.

The maintenance of machinery requires its operational understanding and a toolbox for repair. The methods for the precision engineering of native proteins meet a similar requirement in biosystems. Its success hinges on the principles regulating chemical reactions with a protein. Here, we report a technology that delivers high-level control over reactivity, chemoselectivity, site-selectivity, modularity, dual-probe installation, and protein-selectivity. It utilizes cysteine-based chemoselective Linchpin-Directed site-selective Modification of lysine residue in a protein (LDMC-K). The efficiency of the end-user-friendly protocol is evident in quantitative conversions within an hour. A chemically orthogonal C-S bond-formation and bond-dissociation are essential among multiple regulatory attributes. The method offers protein selectivity by targeting a single lysine residue of a single protein in a complex biomolecular mixture. The protocol renders analytically pure single-site probe-engineered protein bioconjugate. Also, it provides access to homogeneous antibody conjugates (AFC and ADC). The LDMC-K-ADC exhibits highly selective anti-proliferative activity towards breast cancer cells.

Neuropsychiatric symptoms of dementia and caregivers' burden: a study among Indian caregivers / Sintomas neuropsiquiátricos de demência e sobrecarga dos cuidadores: um estudo entre cuidadores indianos

ABSTRACT Dementia is considered a most serious and disabling condition, affecting both the individual suffering from it and their caregiver. Objective: The study aimed to evaluate the relationship between neuropsychiatric problems of dementia and caregiver burden. Methods: A total of 138 caregivers of people with dementia participated in this cross-sectional study. The caregivers completed the questionnaires containing sociodemographic information as well as neuropsychiatric problems of dementia and caregiver burden. Results: The findings showed that all of the care-recipients were suffering from some kind of neuropsychiatric symptoms, the most common being apathy, anxiety, motor disturbance, and hallucination. Out of 12 symptoms, 11 were significantly associated with caregivers' burden. The most important finding is that the severity of neuropsychiatric symptoms is highly responsible for severe caregivers' burden. Conclusions: The identification of neuropsychiatric symptoms of dementia that influence caregiver burden is very critical for both caregivers' and care-recipients' health perspective. These findings can also be utilized to create care settings for demented people and help determine policies in the future.

RESUMO A demência é considerada a condição mais grave e incapacitante que afeta ao mesmo tempo tanto o indivíduo que a sofre como o seu cuidador. Objetivo: O estudo tem como objetivo avaliar a relação entre problemas neuropsiquiátricos de demência e sobrecarga do cuidador. Métodos: 138 cuidadores de pessoas com demência participaram do estudo transversal. Os cuidadores preencheram os questionários contendo informações sociodemográficas, bem como problemas neuropsiquiátricos de demência e sobrecarga do cuidador. Resultados: Observou-se que todos os atendidos apresentavam algum tipo de sintoma neuropsiquiátrico; os mais comuns foram apatia, ansiedade, distúrbios motores e alucinações. Com exceção de um sintoma, 11 outros sintomas foram significativamente associados à sobrecarga dos cuidadores. O achado mais importante é que a gravidade dos sintomas neuropsiquiátricos é altamente responsável pela sobrecarga dos cuidadores. Conclusões: A identificação de sintomas neuropsiquiátricos de demência que influenciem a sobrecarga do cuidador é muito importante para a perspectiva de saúde dos cuidadores e dos receptores de cuidados. Essas descobertas também podem ser utilizadas para criar ambientes de atendimento para pessoas com demência e ajudar a determinar políticas no futuro.

Selection of start codon during mRNA scanning in eukaryotic translation initiation.

Accurate and high-speed scanning and subsequent selection of the correct start codon are important events in protein synthesis. Eukaryotic mRNAs have long 5' UTRs that are inspected for the presence of a start codon by the ribosomal 48S pre-initiation complex (PIC). However, the conformational state of the 48S PIC required for inspecting every codon is not clearly understood. Here, atomistic molecular dynamics (MD) simulations and energy calculations suggest that the scanning conformation of 48S PIC may reject all but 4 (GUG, CUG, UUG and ACG) of the 63 non-AUG codons, and initiation factor eIF1 is crucial for this discrimination. We provide insights into the possible role of initiation factors eIF1, eIF1A, eIF2α and eIF2ß in scanning. Overall, the study highlights how the scanning conformation of ribosomal 48S PIC acts as a coarse selectivity checkpoint for start codon selection and scans long 5' UTRs in eukaryotic mRNAs with accuracy and high speed.

Neuropsychiatric symptoms of dementia and caregivers' burden: a study among Indian caregivers.

Dementia is considered a most serious and disabling condition, affecting both the individual suffering from it and their caregiver. Objective: The study aimed to evaluate the relationship between neuropsychiatric problems of dementia and caregiver burden. Methods: A total of 138 caregivers of people with dementia participated in this cross-sectional study. The caregivers completed the questionnaires containing sociodemographic information as well as neuropsychiatric problems of dementia and caregiver burden. Results: The findings showed that all of the care-recipients were suffering from some kind of neuropsychiatric symptoms, the most common being apathy, anxiety, motor disturbance, and hallucination. Out of 12 symptoms, 11 were significantly associated with caregivers' burden. The most important finding is that the severity of neuropsychiatric symptoms is highly responsible for severe caregivers' burden. Conclusions: The identification of neuropsychiatric symptoms of dementia that influence caregiver burden is very critical for both caregivers' and care-recipients' health perspective. These findings can also be utilized to create care settings for demented people and help determine policies in the future.

A demência é considerada a condição mais grave e incapacitante que afeta ao mesmo tempo tanto o indivíduo que a sofre como o seu cuidador. Objetivo: O estudo tem como objetivo avaliar a relação entre problemas neuropsiquiátricos de demência e sobrecarga do cuidador. Métodos: 138 cuidadores de pessoas com demência participaram do estudo transversal. Os cuidadores preencheram os questionários contendo informações sociodemográficas, bem como problemas neuropsiquiátricos de demência e sobrecarga do cuidador. Resultados: Observou-se que todos os atendidos apresentavam algum tipo de sintoma neuropsiquiátrico; os mais comuns foram apatia, ansiedade, distúrbios motores e alucinações. Com exceção de um sintoma, 11 outros sintomas foram significativamente associados à sobrecarga dos cuidadores. O achado mais importante é que a gravidade dos sintomas neuropsiquiátricos é altamente responsável pela sobrecarga dos cuidadores. Conclusões: A identificação de sintomas neuropsiquiátricos de demência que influenciem a sobrecarga do cuidador é muito importante para a perspectiva de saúde dos cuidadores e dos receptores de cuidados. Essas descobertas também podem ser utilizadas para criar ambientes de atendimento para pessoas com demência e ajudar a determinar políticas no futuro.

Insight into the Mechanism of Carrier-Mediated Delivery of siRNA in the Cell Membrane Using MD Simulation.

The effective translocation of small interfering RNA (siRNA) across cell membranes has become one of the main challenges in gene silencing therapy. In this study, we have carried out molecular dynamics simulations to investigate a systematic procedure with different carriers that could be convenient for efficient siRNA delivery into the cell. Starting with poly-amido-amine (PAMAM) dendrimers and cholesterol molecules as carriers, we have found cholesterol as the most efficient carrier for siRNA when it is covalently attached with the siRNA terminal group. Our simulations show that binding of this complex in the lipid membrane alters the structure and dynamics of the nearby lipids to initiate the translocation process. Potential of mean force (PMF) was computed for siRNA with the carriers along the bilayer normal to understand the spontaneity of the process. Though all the PMF profiles show repulsive interaction inside the bilayer, the siRNA with cholesterol shows a comparative attractive interaction (∼27 kcal/mol) with respect to the siRNA-PAMAM complex. Altogether, our results demonstrate the binding interaction of the siRNA-carrier complex in the lipid membrane and propose a theoretical model for the efficient carrier by comparative study of the binding. The probable mechanism of the translocation process is also provided by the alteration of the lipid structure and dynamics for specifically siRNA-cholesterol binding.

Correlation of visceral body fat with waist-hip ratio, waist circumference and body mass index in healthy adults: A cross sectional study.

BACKGROUND: Visceral Fat (VF) is the underlying culprit for cardiovascular diseases, type 2 diabetes, breast cancer, etc. VF can be estimated at present only by using expensive instruments as Bio Impedance Analyzer (BIA), DEXA scanner, etc. Measurement of Waist-Hip Ratio (WHR) can be used as a proxy for VF. Hence, the present study was done to assess the role of WHR as appropriate technology for assessment of VF. The aim of this study was to find correlation of Visceral Fat Area (VFA) with (WHR), Waist Circumference (WC) and Body Mass Index (BMI) in young healthy adults. METHODS: It was a descriptive cross-sectional study conducted on 215 healthy adults over one year in Western Maharashtra. Biospace 720 was used to assess VF. Data was analyzed by using software SPSS version 20.0. In body 720 was used to assess VF of subjects. RESULTS: Majority 155 (73%) were males and 57 (27%) were females. Nearly half (42% of males, 49% of females) had VFA above cut off value (i.e. 100 cm2) and 42% of males had WHR >0.9 and 56% of females had WHR >0.8. We found a very strong correlation between VFA and WHR (r = 0.936, p < 0.05) among males and females (r = 0.920, p < 0.05) and correlation between WC and BMI with VFA (r = 0.739, r = 0.758) for males, (r = 0.774, r = 0.605) for females was modest. CONCLUSION: There is a strong correlation between VF and WHR. Measurement of WHR is simple, handy, and inexpensive tool which can be used as a surrogate to measure VF.

Insights into the behavioral difference of water in the presence of GM1.

Studies on the structure and dynamics of interfacial water, emphasizing on the properties of water near the surface of biomolecules, are well reported, but there is a lack of evidence on the behavior of water near a comparatively rough surface containing molecules with a bulky head group like GM1. In this report we comparatively analyze the structure and dynamics of water as a function of distance from the lipid head group in GM1 containing lipid bilayers, with the lipid bilayers where GM1 is not present. This approach effectively demonstrates the behavioral difference and hence delayed convergence from bound water to bulk water in the presence of GM1 compared to a relatively smooth surface.

In silico phase separation in the presence of GM1 in ternary and quaternary lipid bilayers.

Cell membranes are multi-component mixtures with structural and compositional heterogeneity exhibiting a complex phase behavior. Domains formed in cell membranes often known as "Rafts" are of immense importance. Using coarse grained molecular dynamics simulations, we have studied the spontaneous phase separation of the ternary (POPC [1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine]/cholesterol/GM1) and quaternary (POPC/PSM[palmitoyl sphingomyelin]/cholesterol/GM1) lipid bilayers into liquid ordered (Lo) and liquid disordered (Ld) domains due to self-aggregation of GM1 molecules and co-localization of cholesterol with GM1 in accordance with experiments. It is found that GM1 molecules have the ability to associate strongly with each other which leads to the formation of ordered domains in the lipid mixture and the interactions are through the head group and unsaturated tails present in GM1. Preference of cholesterol for association with GM1 over PSM is observed, the domains consisting of GM1 and cholesterol are formed even in the presence of PSM. PSM also forms small domains with cholesterol that are randomly distributed in the Ld phase. Estimation of dynamic quantities like diffusion coefficient also shows that cholesterol has the highest diffusion rate in the Ld phase which is further attributed to its flip flop ability. It is found that in the presence of PSM, cholesterol can undergo flip flop even in the Lo phase. This is accredited to the interaction of cholesterol with PSM from which it can be concluded that in the presence of PSM, the domains formed by GM1 are less tightly packed and less stable than that in the ternary mixture.

Insights into binding of cholera toxin to GM1 containing membrane.

Interactions of cholera toxin (CT) with membrane are associated with the massive secretory diarrhea seen in Asiatic cholera. Ganglioside GM1 has been shown to be responsible for the binding of the B subunit of cholera toxin (CT-B), which then helps CT to pass through the membrane, but the exact mechanism remains to be explored. In this work, we have carried out atomistic scale molecular dynamics simulation to investigate the structural changes of CT upon membrane binding and alteration in membrane structure and dynamics. Starting from the initial structure where the five units of B subunit bind with five GM1, only three of five units remain bound and the whole CT is tilted such that the three binding units are deeper in the membrane. The lipids that are in contact with those units of the CT-B behave differently from the rest of the lipids. Altogether, our results demonstrate the atomistic interaction of CT with GM1 containing lipid membrane and provide a probable mechanism of the early stage alteration of lipid structure and dynamics, which can make a passage for penetration of CT on membrane surface.

Ion channel stability of Gramicidin A in lipid bilayers: effect of hydrophobic mismatch.

Hydrophobic mismatch which is defined as the difference between the lipid hydrophobic thickness and the peptide hydrophobic length is known to be responsible in altering the lipid/protein dynamics. Gramicidin A (gA), a 15 residue ß helical peptide which is well recognized to form ion conducting channels in lipid bilayer, may change its structure and function in a hydrophobic mismatched condition. We have performed molecular dynamics simulations of gA dimer in phospholipid bilayers to investigate whether or not the conversion from channel to non-channel form of gA dimer would occur under extreme negative hydrophobic mismatch. By varying the length of lipid bilayers from DLPC (1, 2-Dilauroyl-sn-glycero-3-phosphocholine) to DAPC (1, 2-Diarachidoyl-sn-glycero-3-phosphocholine), a broad range of mismatch was considered from nearly matching to extremely negative. Our simulations revealed that though the ion-channel conformation is retained by gA under a lesser mismatched situation, in extremely negative mismatched situation, in addition to bilayer thinning, the conformation of gA is changed and converted to a non-channel one. Our results demonstrate that although the channel conformation of Gramicidin A is the most stable structure, it is possible for gA to change its conformation from channel to non-channel depending upon the local environment of host bilayers.