Interaction preferences between nucleobase mimetics and amino acids in aqueous solutions

Coding From Binding? Molecular Interactions at the Heart of Translation

The mechanism and the evolution of DNA replication and transcription, the key elements of the central dogma of biology, are fundamentally well explained by the physicochemical complementarity between strands of nucleic acids. However, the determinants that have shaped the third part of the dogma-the process of biological translation and the universal genetic code-remain unclear. We review and seek parallels between different proposals that view the evolution of translation through the prism of weak, noncovalent interactions between biological macromolecules. In particular, we focus on a recent proposal that there exists a hitherto unrecognized complementarity at the heart of biology, that between messenger RNA coding regions and the proteins that they encode, especially if the two are unstructured. Reflecting the idea that the genetic code evolved from intrinsic binding propensities between nucleotides and amino acids, this proposal promises to forge a link between the distant past and the present of biological systems.

Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium

A vast number of intracellular membraneless bodies also known as biomolecular condensates form through a liquid-liquid phase separation (LLPS) of biomolecules. To date, phase separation has been identified as the main driving force for a membraneless organelles such as nucleoli, Cajal bodies, stress granules, and chromatin compartments. Recently, the protein-RNA condensation is receiving increased attention, because it is closely related to the biological function of cells such as transcription, translation, and RNA metabolism. Despite the multidisciplinary efforts put forth to study the biophysical properties of protein-RNA condensates, there are many fundamental unanswered questions regarding the mechanism of formation and regulation of protein-RNA condensates in eukaryotic cells. Major challenges in studying protein-RNA condensation stem from (i) the molecular heterogeneity and conformational flexibility of RNA and protein chains and (ii) the nonequilibrium nature of transcription and cellular environment. Computer simulations, bioinformatics, and mathematical models are uniquely positioned for shedding light on the microscopic nature of protein-RNA phase separation. To this end, there is an urgent need for innovative models with the right spatiotemporal resolution for confronting the experimental observables in a comprehensive and physics-based manner. In this chapter, we will summarize the currently emerging research efforts, which employ atomistic and coarse-grained molecular models and field theoretical models to understand equilibrium and nonequilibrium aspects of protein-RNA condensation.

Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses

During packaging in positive-sense single-stranded RNA (+ssRNA) viruses, coat proteins (CPs) interact directly with multiple regions in genomic RNA (gRNA), but the underlying physicochemical principles remain unclear. Here we analyze the high-resolution cryo-EM structure of bacteriophage MS2 and show that the gRNA/CP binding sites, including the known packaging signal, overlap significantly with regions where gRNA nucleobase-density profiles match the corresponding CP nucleobase-affinity profiles. Moreover, we show that the MS2 packaging signal corresponds to the global minimum in gRNA/CP interaction energy in the unstructured state as derived using a linearly additive model and knowledge-based nucleobase/amino-acid affinities. Motivated by this, we predict gRNA/CP interaction sites for a comprehensive set of 1082 +ssRNA viruses. We validate our predictions by comparing them with site-resolved information on gRNA/CP interactions derived in SELEX and CLIP experiments for 10 different viruses. Finally, we show that in experimentally studied systems CPs frequently interact with autologous coding regions in gRNA, in agreement with both predicted interaction energies and a recent proposal that proteins in general tend to interact with own mRNAs, if unstructured. Our results define a self-consistent framework for understanding packaging in +ssRNA viruses and implicate interactions between unstructured gRNA and CPs in the process.

Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease caused by the misfolding of Cu, Zn superoxide dismutase (SOD1). Several earlier studies have shown that monomeric apo SOD1 undergoes significant local unfolding dynamics and is the predecessor for aggregation. Here, we have employed atomistic molecular dynamics (MD) simulations to study the structure and dynamics of monomeric apo and holo SOD1 in water, aqueous urea and aqueous urea-TMAO (trimethylamine oxide) solutions. Loop IV (zinc-binding loop) and loop VII (electrostatic loop) of holo SOD1 are considered as functionally important loops as they are responsible for the structural stability of holo SOD1. We found larger local unfolding of loop IV and VII of apo SOD1 as compared to holo SOD1 in water. Urea induced more unfolding in holo SOD1 than apo SOD1, whereas the stabilization of both the form of SOD1 was observed in ternary solution (i.e. water/urea/TMAO solution) but the extent of stabilization was higher in holo SOD1 than apo SOD1. The partially unfolded structures of apo SOD1 in water, urea and holo SOD1 in urea were identified by the exposure of the hydrophobic cores, which are highly dynamic and these may be the initial events of aggregation in SOD1. Our simulation studies support the formation of aggregates by means of the local unfolding of monomeric apo SOD1 as compared to holo SOD1 in water.

Frameshifting preserves key physicochemical properties of proteins

Frameshifts in protein coding sequences are widely perceived as resulting in either nonfunctional or even deleterious protein products. Indeed, frameshifts typically lead to markedly altered protein sequences and premature stop codons. By analyzing complete proteomes from all three domains of life, we demonstrate that, in contrast, several key physicochemical properties of protein sequences exhibit significant robustness against +1 and -1 frameshifts. In particular, we show that hydrophobicity profiles of many protein sequences remain largely invariant upon frameshifting. For example, over 2,900 human proteins exhibit a Pearson's correlation coefficient R between the hydrophobicity profiles of the original and the +1-frameshifted variants greater than 0.7, despite an average sequence identity between the two of only 6.5% in this group. We observe a similar effect for protein sequence profiles of affinity for certain nucleobases as well as protein sequence profiles of intrinsic disorder. Finally, analysis of significance and optimality demonstrates that frameshift stability is embedded in the structure of the universal genetic code and may have contributed to shaping it. Our results suggest that frameshifting may be a powerful evolutionary mechanism for creating new proteins with vastly different sequences, yet similar physicochemical properties to the proteins from which they originate.

Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein

α-Synuclein is an intrinsically disordered protein whose function in a healthy brain is poorly understood. It is genetically and neuropathologically linked to Parkinson's disease (PD). PD is manifested after the accumulation of plaques of α-synuclein aggregates in the brain cells. Aggregates of α-synuclein are very toxic and lead to the disruption of cellular homeostasis and neuronal death. α-Synuclein can also contribute to disease propagation as it may exert noxious effects on neighboring cells. Understanding the mechanism of α-synuclein aggregation will facilitate the problem of dealing with neurodegenerative diseases in general and that of PD in particular. Here, we have used molecular dynamics simulations to investigate the behavior of α-synuclein at various temperatures and in different concentrations of urea and trimethyl amine oxide. The residue region from 61 to 95 of α-synuclein is experimentally known as amyloidogenic. In our study, we have identified some other regions, which also have the propensity to form an aggregate besides this known sequence. Urea being a denaturant interacts more with these regions of α-synuclein through hydrogen bond formation and inhibits the β-sheet formation, whereas trimethyl amine oxide itself does not interact much with the protein and stabilizes the protein by preferentially distributing water molecules on the surface of the protein.

RNA-protein interactions in an unstructured context

Despite their importance, our understanding of noncovalent RNA-protein interactions is incomplete. This especially concerns the binding between RNA and unstructured protein regions, a widespread class of such interactions. Here, we review the recent experimental and computational work on RNA-protein interactions in an unstructured context with a particular focus on how such interactions may be shaped by the intrinsic interaction affinities between individual nucleobases and protein side chains. Specifically, we articulate the claim that the universal genetic code reflects the binding specificity between nucleobases and protein side chains and that, in turn, the code may be seen as the Rosetta stone for understanding RNA-protein interactions in general.

mRNA/protein sequence complementarity and its determinants: The impact of affinity scales

It has recently been demonstrated that the nucleobase-density profiles of mRNA coding sequences are related in a complementary manner to the nucleobase-affinity profiles of their cognate protein sequences. Based on this, it has been proposed that cognate mRNA/protein pairs may bind in a co-aligned manner, especially if unstructured. Here, we study the dependence of mRNA/protein sequence complementarity on the properties of the nucleobase/amino-acid affinity scales used. Specifically, we sample the space of randomly generated scales by employing a Monte Carlo strategy with a fitness function that depends directly on the level of complementarity. For model organisms representing all three domains of life, we show that even short searches reproducibly converge upon highly optimized scales, implying that the topology of the underlying fitness landscape is decidedly funnel-like. Furthermore, the optimized scales, generated without any consideration of the physicochemical attributes of nucleobases or amino acids, resemble closely the nucleobase/amino-acid binding affinity scales obtained from experimental structures of RNA-protein complexes. This provides support for the claim that mRNA/protein sequence complementarity may indeed be related to binding between the two. Finally, we characterize suboptimal scales and show that intermediate-to-high complementarity can be reached by substantially diverse scales, but with select amino acids contributing disproportionally. Our results expose the dependence of cognate mRNA/protein sequence complementarity on the properties of the underlying nucleobase/amino-acid affinity scales and provide quantitative constraints that any physical scales need to satisfy for the complementarity to hold.

Messenger RNAs and proteins, two essential types of biopolymers, have recently been shown to exhibit closely related, complementary physicochemical properties. Specifically, density profiles of certain groups in messenger RNA sequences directly match the affinity profiles for precisely those groups in protein sequences they encode. Based on this, it has been suggested that these molecules may interact with each other specifically and in a co-aligned fashion, especially when unstructured. Here, we explore different amino-acid scales used in the above analysis to assess which of their properties dictate the observed matching. Specifically, we define the constraints that need to be satisfied by physical scales for the complementarity to hold and show that the previously derived nucleobase/amino-acid affinity scales indeed satisfy these constraints. As a whole, our work provides a quantitative foundation for understanding the putative messenger RNA/protein complementarity with implications in different areas of RNA/protein biology including transcription, translation, splicing and viral assembly.

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments.

Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β42 monomer: insights from molecular dynamics simulations

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β₄₂ (Aβ₄₂) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ₄₂ aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ₄₂. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ₄₂ by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ₄₂ monomer. Overall, MD simulations reveal that C1 inhibits Aβ₄₂ aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ₄₂.

Inosine Nucleobase Acts as Guanine in Interactions with Protein Side Chains

A central intermediate in purine catabolism, the inosine nucleobase hypoxanthine is also one of the most abundant modified nucleobases in RNA and plays key roles in the regulation of gene expression and determination of cell fate. It is known that hypoxanthine acts as guanine when interacting with other nucleobases and base pairs most favorably with cytosine. However, its preferences when it comes to interactions with amino acids remain unknown. Here we present for the first time the absolute binding free energies and the associated interaction modes between hypoxanthine and all standard, non-glycyl/non-prolyl amino acid side chain analogs as derived from molecular dynamics simulations and umbrella sampling in high- and low-dielectric environments. We illustrate the biological relevance of the derived affinities by providing a quantitative explanation for the specificity of hypoxanthine-guanine phosphoribosyltransferase, a key enzyme in the purine salvage pathway. Our results demonstrate that in its affinities for protein side chains, hypoxanthine closely matches guanine, much more so than its precursor adenine.

The progene hypothesis: the nucleoprotein world and how life began

In this article, I review the results of studies on the origin of life distinct from the popular RNA world hypothesis. The alternate scenario postulates the origin of the first bimolecular genetic system (a polynucleotide gene and a polypeptide processive polymerase) with simultaneous replication and translation and includes the following key features: 1. The bimolecular genetic system emerges not from mononucleotides and monoamino acids, but from progenes, namely, trinucleotides aminoacylated on 3'-end by a non-random amino acid (NpNpNp ~ pX ~ Aa, where N--deoxyribo- or ribonucleoside, p--phosphate, X--a bifunctional agent, for example ribose, Aa--amino acid, ~ macroerge bond). Progenes are used as substrates for simultaneous synthesis of a polynucleotide and a polypeptide. Growth of the system is controlled by the growing polypeptide, and the bimolecular genetic system emerges as an extremely rare event. The first living being (virus-like organism protoviroid, Protoviroidum primum) arises and reproduces in prebiotic liposome-like structures using progenes. A population of protoviroids possessing the genetic system evolves in accordance with the Darwinian principle. Early evolution from protoviroid world to protocell world is shortly described. 2. The progene forming mechanism (NpNp + Np ~ pX ~ Aa) makes it possible to explain the emergence of the prebiotic physicochemical group genetic code, as well as the selection of organic compounds for the future genetic system from the racemic environment. 3. The protoviroid is reproduced on a progene basis via replicative transcription-translation (RTT, the first molecular genetic process) that is similar to its modern counterparts. Nothing is required for the emergence and reproduction of the protoviroid except for progenes and conditions for their formation. 4. The general scheme of early evolution is as follows: prebiotic world → protoviroid (nucleoprotein) world → protocell (DNA-RNA-protein) world → LUCA (Last Universal Common Ancestor) → modern cell world. This scheme exclude the existence of an independent RNA world as predecessor of the cellular world.