Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms

Intrinsically disordered proteins (IDPs) lack well-defined secondary or tertiary structures in solution but are found to be involved in a wide range of critical cellular processes that highlight their functional importance. IDPs usually undergo folding upon binding to their targets. Such binding coupled to folding behavior has widened our perspective on the protein structure-dynamics-function paradigm in molecular biology. However, characterizing the folding upon binding mechanism of IDPs experimentally remains quite challenging. Molecular simulations emerge as a potentially powerful tool that offers information complementary to experiments. Here we present a general computational framework for the molecular simulations of IDP folding upon binding processes that combines all-atom molecular dynamics (MD) and coarse-grained simulations. The classical all-atom molecular dynamics approach using GPU acceleration allows the researcher to explore the properties of the IDP conformational ensemble, whereas coarse-grained structure-based models implemented with parameters carefully calibrated to available experimental measurements can be used to simulate the entire folding upon binding process. We also discuss a set of tools for the analysis of MD trajectories and describe the details of the computational protocol to follow so that it can be adapted by the user to study any IDP in isolation and in complex with partners.

Application of native mass spectrometry in studying intrinsically disordered proteins: A special focus on neurodegenerative diseases

Intrinsically disordered proteins (IDPs) are integral part of the proteome, regulating vital biological processes. Such proteins gained further visibility due to their key role in neurodegenerative diseases and cancer. IDPs however, escape structural characterization by traditional biophysical tools owing to their extreme flexibility and heterogeneity. In this review, we discuss the advantages of native mass spectrometry (MS) in analysing the atypical conformational dynamics of IDPs and recent advances made in the field. Especially, MS studies unravelling the conformational facets of IDPs involved in neurodegenerative diseases are highlighted. The limitations and the future promises of native MS while studying IDPs have been discussed.

Globular protein backbone conformational disorder in crystal structures

Proteins are not static molecules but dynamic entities able to modify their structure for several reasons, from the necessity to recognize partners to the regulation of their thermodynamic stability. Conformational disorder is frequent in protein structures and atoms can have, in protein crystal structures, two or more alternative, equilibrium positions close to each other. Here, a set of protein crystal structures refined at very high resolution (1 Å or better) is examined to characterize the conformational disorder of the backbone atoms, which is not infrequent: about 15% of the protein backbone atoms are conformationally disordered and three quarters of them have been deposited with two or more equilibrium positions (most of the others were not detected in the electron density maps). Several structural features have been examined and it was observed that Cα atoms tend to be disordered more frequently than the other backbone atoms, likely because their disorder is induced by disordered side chains: side-chain disorder is two times more frequent than backbone disorder. Surprisingly, backbone disorder is only slightly more frequent in loops than in helices and strands and this is in agreement with the observation that backbone disorder is a localized phenomenon: in about 80% of the cases, it is observed in one amino acid and not in its neighbors. However, although backbone disorder does not cluster along the polypeptide sequence, it tends to cluster in 3D, since backbone-disordered amino acids distant in sequence are close in the 3D space.

Imaging phospholipid conformational disorder and packing in giant multilamellar liposome by confocal Raman microspectroscopy

Liposomes are closed phospholipid bilayer systems that have profound applications in fundamental cell biology, pharmaceutics and medicine. Depending on the composition (pure or mixture of phospholipids, presence of cholesterol) and preparation protocol, intra- and inter-chain molecular interactions vary leading to changes in the quality (order and packing) of liposomes. So far it is not possible to image conformational disorders and packing densities within a liposome in a straightforward manner. In this study, we utilized confocal Raman microspectroscopy to visualize structural disorders and packing efficiency within a giant multilamellar liposome model by focusing mainly on three regions in the vibrational spectrum (CC stretching, CH deformation and CH stretching). We estimated properties such as trans/gauche isomers and lateral packing probability. Interestingly, our Raman imaging studies revealed gel phase rich domains and heterogeneous lateral packing within the giant multilamellar liposome.

Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users

It is often necessary to build subsets of the Protein Data Bank to extract structural trends and average values. For this purpose it is mandatory that the subsets are non-redundant and of high quality. The first problem can be solved relatively easily at the sequence level or at the structural level. The second, on the contrary, needs special attention. It is not sufficient, in fact, to consider the crystallographic resolution and other feature must be taken into account: the absence of strings of residues from the electron density maps and from the files deposited in the Protein Data Bank; the B-factor values; the appropriate validation of the structural models; the quality of the electron density maps, which is not uniform; and the temperature of the diffraction experiments. More stringent criteria produce smaller subsets, which can be enlarged with more tolerant selection criteria. The incessant growth of the Protein Data Bank and especially of the number of high-resolution structures is allowing the use of more stringent selection criteria, with a consequent improvement of the quality of the subsets of the Protein Data Bank.

Proteostasis in pediatric pulmonary pathology

Protein homeostasis describes the tight supervision of protein synthesis, correct protein maturation and folding, as well as the timely disposal of unwanted and damaged proteins by the ubiquitin-proteasome pathway or the lysosome-autophagy route. The cellular processes involved in preservation of protein homeostasis are collectively called proteostasis. Dysregulation of proteostasis is an emerging common pathomechanism for chronic lung diseases in the adult and aged patient. There is also rising evidence that impairment of protein homeostasis contributes to early sporadic disease onset in pediatric lung diseases beyond the well-known hereditary proteostasis disorders such as cystic fibrosis and alpha-1 antitrypsin (AAT) deficiency. Identifying the pathways that contribute to impaired proteostasis will provide new avenues for therapeutic interference with the pathogenesis of chronic lung diseases in the young and adult. Here, we introduce the concept of proteostasis and summarize available evidence on dysregulation of proteostasis pathways in pediatric and adult chronic lung diseases.

A study of the oxidation-induced conformational and functional changes in neuroserpin

BACKGROUND

Neuroserpin, a member of the Serine Proteinase Inhibitor (Serpin) superfamily, is known to be a neuroprotective factor in the focal ischemic stroke followed by reducing the microglial activation. Neuroserpin is a protein rich of methionine residues that can scavenge the free radical species which may increase its neuroprotective effect. On the other hand, the oxidative modifications of the amino acid residues in neuroserpin may lead to changes in its conformation and function. In this study, it was investigated the changes in the conformation and the function of the oxidized neuroserpin.

METHODS

Neuroserpin expressed in E. coli, BL21 or M15 harboring plasmid pQE81L containing neuroserpin cDNA. Expressed neuroserpin was purified by resin sulfopropyl A50 precharged with 0.1 M NiSO4 under denaturing condition. Neuroserpin was oxidized under oxidative stress condition in the presence of different concentration of hydrogen peroxide. The oxidation of neuroserpin was conveniently detected by a carbonyl content assay using 2, 4 dinitrophenylhydrazine. Changes in tertiary structure of neuroserpin were monitored by spectrofluorimeter to study the alteration of intrinsic fluorescence and also fluorescence of 8-anilinonaphthalin-1 sulfonic acid (ANS) in native and oxidized form of neuroserpin.

RESULTS

Total expressed neuroserpin was estimated 4-5 mg/lit in 2XYT culture media. SDS-PAGE analysis of purified neuroserpin showed a single band which reflects the efficiency of the resin SP A50 for purification of the proteins containing 6xHis tag. Carbonyl content of oxidized and native neuroserpin was estimated 12.3 +/- 0.3 and 0.45 +/- 0.05, respectively. The inhibitory activity of oxidized neuroserpin decreased up to 40-60% as compared with native form of neuroserpin. Intrinsic fluorescence and also the emission of ANS bind to the hydrophobic region of the protein altered from 380 to 85 and in the case of ANS from 105 to 150 in oxidized and native form of neuroserpin, respectively.

CONCLUSION

The decreased intrinsic fluorescence intensity, an enhancement in the fluorescence of ANS, and loss of the inhibitory activity up to 40-60% in neuroserpin, all suggested a conformational modification in the protein under the oxidative stress condition. Remaining the inhibitory activity of neuroserpin reflects that the protein tolerates the oxidative stress condition effectively.