Adenosine triphosphate energy‐independently controls protein homeostasis with unique structure and diverse mechanisms

Abstract

Proteins function in the crowded cellular environments with high salt concentrations, thus facing tremendous challenges of misfolding/aggregation which represents a pathological hallmark of aging and an increasing spectrum of human diseases. Recently, intrinsically disordered regions (IDRs) were recognized to drive liquid–liquid phase separation (LLPS), a common principle for organizing cellular membraneless organelles (MLOs). ATP, the universal energy currency for all living cells, mysteriously has concentrations of 2–12 mM, much higher than required for its previously‐known functions. Only recently, ATP was decoded to behave as a biological hydrotrope to inhibit protein LLPS and aggregation at mM. We further revealed that ATP also acts as a bivalent binder, which not only biphasically modulates LLPS driven by IDRs of human and viral proteins, but also bind to the conserved nucleic‐acid‐binding surfaces of the folded proteins. Most unexpectedly, ATP appears to act as a hydration mediator to antagonize the crowding‐induced destabilization as well as to enhance folding of proteins without significant binding. Here, this review focuses on summarizing the results of these biophysical studies and discussing their implications in an evolutionary context. By linking triphosphate with unique hydration property to adenosine, ATP appears to couple the ability for establishing hydrophobic, π‐π, π‐cation and electrostatic interactions to the capacity in mediating hydration of proteins, which is at the heart of folding, dynamics, stability, phase separation and aggregation. Consequently, ATP acquired a category of functions at ~mM to energy‐independently control protein homeostasis with diverse mechanisms, thus implying a link between cellular ATP concentrations and protein‐aggregation diseases.

Structural basis of anti-SARS-CoV-2 activity of HCQ: specific binding to N protein to disrupt its interaction with nucleic acids and LLPS

“…At the fundamental level of molecular interactions, the core mechanisms for LLPS induced by nucleic acids appear to be relatively conserved (10,14,15). In particular, the significantly perturbed residues of NTD and CTD upon binding HCQ are completely identical in all variants of SARS-CoV-2, as well as even highly conserved in SARS-CoV-1 (Fig.…”

“…The current results suggest that the ability of HCQ to specifically disrupt LLPS of N protein induced by nucleic acids may at least partly contribute to the inhibition of the maturation of SARS-CoV-2 virions. To the best of our knowledge, HCQ is the first drug which has been revealed to target LLPS, thus bearing the unprecedented implications for further design of drugs in general by modulating LLPS, whose roles in underlying various human diseases are starting to be recognized (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15).…”

“…Very recently, liquid-liquid phase separation (LLPS), the emerging principle for commonly organizing the membrane-less organelles (MLOs) or compartments critical for cellular physiology and pathology (11)(12)(13)(14)(15), has been identified as the key mechanism underlying the diverse functions of SARS-CoV-2 N protein (5)(6)(7)(8)(9)(10). Nevertheless, all identified functions of N proteins so far appear to be dependent on its capacity in binding various nucleic acids with both specific and non-specific sequences.…”

Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders

“…Voltage-dependent anion channels (VDACs) located in the mitochondrial outer membrane (MOM) [ 41 ] and adenine nucleotide translocators (ANTs) on the inner mitochondrial membranes (IMM) [ 42 , 43 ] facilitate the export of ATP into cytosol where ATP accumulation has been observed to be the highest [ 44 ]. The high physiological concentration of ATP in cytoplasm may be used to control the pathological aggregation of macromolecules that coacervate as a result of transient interactions during LLPS in the cytoplasm and nucleus [ 45 , 46 ]. A major hallmark of ALS/FTD is the presence of FUS inclusion in the cytoplasm.…”

“…Biomolecular condensates adapt to changing endogenous or exogenous conditions [ 3 ] by continuously fine-tuning biochemical reactions, enriching or excluding biomolecules from their environment [ 7 ]. The rapid translocation of mitochondrial ATP synthase to lipid rafts may be integral to these adaptive responses because ATP functions not only as a biological hydrotrope [ 30 , 178 ], increasing the solubility of positively charged, intrinsically disordered proteins [ 179 ], but may act as a universal and specific regulator of intrinsically disordered regions (IDRs) capable of altering physicochemical properties, conformation dynamics, assembly, and aggregation [ 45 ], in addition to providing phosphates as an energy source to fuel post-translational modifications that regulate the fluctuation of biomolecule phase separation during condensate formation [ 79 , 178 ].…”