Sequence patterns and HMM profiles to predict proteome wide zinc finger motifs

Zinc finger (ZnF) is an important class of nucleic acid and protein recognition domain, wherein, zinc ion is the inorganic co-factor that forms a tetrahedral geometry with the cysteine and/or histidine residues. ZnF domains take up diverse architectures with different ZnF motifs and have a wide range of biological functions. Nonetheless, predicting the ZnF motif(s) from the sequence is quite challenging. To this end, 74 unique ZnF sequence patterns are collected from the literature and classified into 32 different classes. Since the shorter length of ZnF sequence patterns leads to inaccurate predictions, ZnF domain Pfam HMM profiles defined under 6 ZnF Pfam clans (215 HMM profiles) and a few undefined Pfam clans (74 HMM profiles) are used for the prediction. A web server, namely, ZnF-Prot (https://project.iith.ac.in/znprot/) is developed which can predict the presence of 31 ZnF domains in a protein/proteome sequence of any organism. The use of ZnF sequence patterns and Pfam HMM profiles resulted in an accurate prediction of 610 test cases (taken randomly from 249 organisms) considered here. Additionally, the application of ZnF-Prot is demonstrated by considering Arabidopsis thaliana, Homo sapiens, Saccharomyces cerevisiae, Caenorhabditis elegans and Ciona intestinalis proteomes as test cases, wherein, 87–96% of the predicted ZnF motifs are cross-validated

Metal ions shape α-synuclein

α-Synuclein is an intrinsically disordered protein that can self-aggregate and plays a major role in Parkinson’s disease (PD). Elevated levels of certain metal ions are found in protein aggregates in neurons of people suffering from PD, and environmental exposure has also been linked with neurodegeneration. Importantly, cellular interactions with metal ions, particularly Ca2+, have recently been reported as key for α-synuclein’s physiological function at the pre-synapse. Here we study effects of metal ion interaction with α-synuclein at the molecular level, observing changes in the conformational behaviour of monomers, with a possible link to aggregation pathways and toxicity. Using native nano-electrospray ionisation ion mobility-mass spectrometry (nESI-IM-MS), we characterize the heterogeneous interactions of alkali, alkaline earth, transition and other metal ions and their global structural effects on α-synuclein. Different binding stoichiometries found upon titration with metal ions correlate with their specific binding affinity and capacity. Subtle conformational effects seen for singly charged metals differ profoundly from binding of multiply charged ions, often leading to overall compaction of the protein depending on the preferred binding sites. This study illustrates specific effects of metal coordination, and the associated electrostatic charge patterns, on the complex structural space of the intrinsically disordered protein α-synuclein

Deciphering Pathways for Carotenogenesis in Haloarchaea

Bacterioruberin and its derivatives have been described as the major carotenoids produced by haloarchaea (halophilic microbes belonging to the Archaea domain). Recently, different works have revealed that some haloarchaea synthetize other carotenoids at very low concentrations, like lycopene, lycopersene, cis- and trans-phytoene, cis- and trans-phytofluene, neo-β-carotene, and neo-α-carotene. However, there is still controversy about the nature of the pathways for carotenogenesis in haloarchaea. During the last decade, the number of haloarchaeal genomes fully sequenced and assembled has increased significantly. Although some of these genomes are not fully annotated, and many others are drafts, this information provides a new approach to exploring the capability of haloarchaea to produce carotenoids. This work conducts a deeply bioinformatic analysis to establish a hypothetical metabolic map connecting all the potential pathways involved in carotenogenesis in haloarchaea. Special interest has been focused on the synthesis of bacterioruberin in members of the Haloferax genus. The main finding is that in almost all the genus analyzed, a functioning alternative mevalonic acid (MVA) pathway provides isopentenyl pyrophosphate (IPP) in haloarchaea. Then, the main branch to synthesized carotenoids proceeds up to lycopene from which β-carotene or bacterioruberin (and its precursors: monoanhydrobacterioriberin, bisanhydrobacterioruberin, dihydrobisanhydrobacteriuberin, isopentenyldehydrorhodopsin, and dihydroisopenthenyldehydrorhodopsin) can be made.This work was partially funded by research grants from MINECO Spain (RTI2018-099860-B-I00) and the University of Alicante (VIGROB-309)

Revealing the Role of Electrostatics in Molecular Recognition, Ion Binding and pH-Dependent Phenomena

In this dissertation, we study the role of electrostatics in molecular recognition, ion binding and pH-dependent phenomena. In this work that includes three different research projects, the Poisson-Boltzmann (PB) model is used to describe the biological system and Delphi (which is a popular tool for solving the PB equation (PBE)) to study the electrostatics of biomolecular systems. Chapter two aims to investigate the role of electrostatic forces in molecular recognition. We calculated electrostatic forces between binding partners separated at various distances. To accomplish this goal, we developed a method to find an appropriate direction to move one chain of protein complexes away from its bound position, and then calculated the corresponding electrostatic force as a function of separation distance. Based on the electrostatic force profile (force as a function of distance), we grouped the cases into four distinct categories. Chapter three reports a new release of a computational method, the BION-2 method, that predicts the positions of non-specifically surface-bound ions. The BION-2 utilizes the Gaussian-based treatment of ions within the framework of the modified Poisson–Boltzmann equation, which does not require a sharp boundary between the protein and water phase. Thus, the predictions are done by the balance of the energy of interaction between the protein charges and the corresponding ions and the de-solvation penalty of the ions as they approach the protein. The BION-2 is tested against experimentally determined ions’ positions, demonstrating that it outperforms the old BION and other available tools. Chapter four focuses on computationally investigating the pH-dependent stability of several melanosomal membrane proteins and comparing them to the pH dependence of the stability of TYR. We confirmed that the pH optimum of TYR is neutral, and we also found that proteins that are negative regulators of melanosomal pH are predicted to function optimally at neutral pH. In contrast, positive pH regulators were predicted to have an acidic pH optimum