Abstract Are there any generalized molecular principles of thermal adaptation? Here, integrating the concepts structural bioinformatics, sequence analysis, and classical knot theory, we develop a robust computational framework that seeks for mechanisms adaptation by comparing orthologous mesophilic‐thermophilic mesophilic‐hyperthermophilic proteins remarkable topological similarities, still leads us to context‐independent results. A comprehensive analysis 4741 high‐resolution, non‐redundant...

Precise control of protein and messenger RNA (mRNA) degradation is essential for cellular metabolism homeostasis. Controlled specific both molecular species necessitates their engagements with the respective machineries; this engagement involves a disordered/unstructured segment substrate traversing tunnel machinery accessing catalytic sites. However, while factors influencing have been extensively explored on genome scale, in multiple organisms, such comprehensive understanding remains...

Abstract Do coding and regulatory segments of a gene co‐evolve with each‐other? Seeking answers to this question, here we analyze the case Escherichia coli ribosomal protein S15, that represses its own translation by specifically binding messenger RNA (rpsO mRNA) stabilizing pseudoknot structure at upstream untranslated region, thus trapping ribosome into an incomplete initiation complex. In absence S1 recognizes rpsO promotes melting very pseudoknot. We employ robust statistical method...

Proteins from thermophilic organisms are a matter of immense interest for decades because its application in fields like de-novo protein design, thermostable variants biocatalysts etc. Previous studies have found several sequence and structural adaptations related to thermal stability, while charge reversal study remains ignored. Here we address whether mutations naturally occur mesophilic-thermophilic/hyperthermophilic orthologous proteins. Do they contribute stability? Our systematic on...

Abstract The majority of mRNA degradation occurs co-translationally. Several works in the past elucidated role codon composition regulating co-translational decay. Integration sequence, structure and ribosomal density unravels common regulatory factors translational helps understanding intricate association between these two important processes. Co-translational is a two-step process, involving stalling release for degradation. Our findings highlight Codon Adaptation Index, sequence-level...

mRNA translation and degradation, though distinct physiological processes, exhibit significant overlap, profoundly influencing cellular gene expression protein production. Extensive works in the past has highlighted prevalence of co-translational decay, citing that codon composition within acts as a key regulator. This process, characterized by rapid kinetics, involves translational stalling followed release for orchestrated myriad factors operating either individually or concert. Our...

ABSTRACT Interactions between distantly placed amino acids in the primary chain (long-range) play a very crucial role formation and stabilization of tertiary structure protein, while interactions closely (short-range) mostly stabilize secondary structures. Every protein needs to maintain marginal stability order perform its physiological functions native environment. The requirements for this mesophilic thermophilic proteins are different. Thermophilic need form more as well stable survive...

Abstract Precise control of protein and mRNA degradation is essential for cellular metabolism homeostasis. Controlled specific both molecular species necessitates their engagements with the respective machineries; this engagement involves a disordered/unstructured segment substrate traversing tunnel machinery accessing catalytic sites. Here, we report that mRNAs comprising longer terminal and/or internal unstructured segments have significantly shorter half-lives; lengths 5′ terminal, 3′...

Abstract Codon optimality is a major factor governing translation speed and efficiency, mRNA expression, stability. Presence of optimal codons maintains steady time, while non-optimal can lead to slow peptidyl transfer, prolonged time frequent halt. Owing this, there are co-translational surveillance protein complexes which monitor this process meticulously trigger the release transcript after The closely associated with various degradation enzymes break down these released transcripts....

ABSTRACT Do charge reversal mutations (CRM) naturally occur in mesophilic-thermophilic/hyperthermophilic (M-T/HT) orthologous proteins? they contribute to thermal stability by altering charge-charge interactions? A careful investigation on 1550 M-T/HT protein pairs with remarkable structural and topological similarity extracts the role of buried partially exposed CRMs enhancing stability. Our findings could assist engineering thermo-stable variants proteins. SIGNIFICANCE Protein is one hot...