Enhanced Sampling of Intrinsic Structural Heterogeneity of the BH3-Only Protein Binding Interface of Bcl-xL

Machine Learning Generation of Dynamic Protein Conformational Ensembles

Machine learning has achieved remarkable success across a broad range of scientific and engineering disciplines, particularly its use for predicting native protein structures from sequence information alone. However, biomolecules are inherently dynamic, and there is a pressing need for accurate predictions of dynamic structural ensembles across multiple functional levels. These problems range from the relatively well-defined task of predicting conformational dynamics around the native state of a protein, which traditional molecular dynamics (MD) simulations are particularly adept at handling, to generating large-scale conformational transitions connecting distinct functional states of structured proteins or numerous marginally stable states within the dynamic ensembles of intrinsically disordered proteins. Machine learning has been increasingly applied to learn low-dimensional representations of protein conformational spaces, which can then be used to drive additional MD sampling or directly generate novel conformations. These methods promise to greatly reduce the computational cost of generating dynamic protein ensembles, compared to traditional MD simulations. In this review, we examine recent progress in machine learning approaches towards generative modeling of dynamic protein ensembles and emphasize the crucial importance of integrating advances in machine learning, structural data, and physical principles to achieve these ambitious goals.

Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL

The intrinsically disordered region (IDR) of Bim binds to the flexible cryptic site of Bcl-xL, a pro-survival protein involved in cancer progression that plays an important role in initiating apoptosis. However, their binding mechanism has not yet been elucidated. We have applied our dynamic docking protocol, which correctly reproduced both the IDR properties of Bim and the native bound configuration, as well as suggesting other stable/meta-stable binding configurations and revealed the binding pathway. Although the cryptic site of Bcl-xL is predominantly in a closed conformation, initial binding of Bim in an encounter configuration leads to mutual induced-fit binding, where both molecules adapt to each other; Bcl-xL transitions to an open state as Bim folds from a disordered to an α-helical conformation while the two molecules bind each other. Finally, our data provides new avenues to develop novel drugs by targeting newly discovered stable conformations of Bcl-xL.

Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations

Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system, REST effectively applies tempering only to the degrees of freedom of interest but not the rest of the system ("solvent"), allowing fewer replicas for covering the same temperature range. A key consideration of REST is how the solute-solvent interactions are scaled together with the solute-solute interactions. Here, we critically evaluate the performance of the latest REST2 protocol for sampling large-scale conformation fluctuations of intrinsically disordered proteins (IDPs). The results show that REST2 promotes artificial protein conformational collapse at high effective temperatures, which seems to be a designed feature originally to promote the sampling of reversible folding of small proteins. The collapse is particularly severe with larger IDPs, leading to replica segregation in the effective temperature space and hindering effective sampling of large-scale conformational changes. We propose that the scaling of the solute-solvent interactions can be treated as free parameters in REST, which can be tuned to control the solute conformational properties (e.g., chain expansion) at different effective temperatures and achieve more effective sampling. To this end, we derive a new REST3 protocol, where the strengths of the solute-solvent van der Waals interactions are recalibrated to reproduce the levels of protein chain expansion at high effective temperatures. The efficiency of REST3 is examined using two IDPs with nontrivial local and long-range structural features, including the p53 N-terminal domain and the kinase inducible transactivation domain of transcription factor CREB. The results suggest that REST3 leads to a much more efficient temperature random walk and improved sampling efficiency, which also further reduces the number of replicas required. Nonetheless, our analysis also reveals significant challenges of relying on tempering alone for sampling large-scale conformational fluctuations of disordered proteins. It is likely that more efficient sampling protocols will require incorporating more sophisticated Hamiltonian replica exchange schemes in addition to tempering.

Structural Details of BH3 Motifs and BH3-Mediated Interactions: an Updated Perspective

Apoptosis is a mechanism of programmed cell death crucial in organism development, maintenance of tissue homeostasis, and several pathogenic processes. The B cell lymphoma 2 (BCL2) protein family lies at the core of the apoptotic process, and the delicate balance between its pro- and anti-apoptotic members ultimately decides the cell fate. BCL2 proteins can bind with each other and several other biological partners through the BCL2 homology domain 3 (BH3), which has been also classified as a possible Short Linear Motif and whose distinctive features remain elusive even after decades of studies. Here, we aim to provide an updated overview of the structural features characterizing BH3s and BH3-mediated interactions (with a focus on human proteins), elaborating on the plasticity of BCL2 proteins and the motif properties. We also discussed the implication of these findings for the discovery of interactors of the BH3-binding groove of BCL2 proteins and the design of mimetics for therapeutic purposes.

Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma

Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.

Impact of Deamidation on the Structure and Function of Antiapoptotic Bcl-xL

Bcl-x_L is an antiapoptotic mitochondrial trans-membrane protein, which is known to play a crucial role in the survival of tumor cells. The deamidation of Bcl-x_L is a pivotal switch that regulates its biological function. The potential impact of deamidation on the structure and dynamics of Bcl-x_L is directly linked to the intrinsically disordered region (IDR), which is the main site for post-translational modifications (PTMs). In this study, we explored deamidation-induced conformational changes in Bcl-x_L to gain insight into its loss of function by performing microsecond-long molecular dynamics (MD) simulations. MD simulation outcomes showed that the IDR motion and interaction patterns have changed notably upon deamidation. Principal component analysis (PCA) demonstrates significant differences between wild-type and deamidated Bcl-x_L and suggests that deamidation affects the structure and dynamics of Bcl-x_L. The combination of clustering analysis, H-bond analysis, and PCA revealed changes in conformation, interaction, and dynamics upon deamidation. Differences in contact patterns and essential dynamics that lead to a narrowing in the binding groove (BG) are clear indications of deamidation-induced allosteric effects. In line with previous studies, we show that the IDR plays a very important role in the loss of apoptotic functions of Bcl-x_L while providing a unique perspective on the underlying mechanism of Bcl-x_L deamidation-induced cell death.

Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions

Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in biology and human diseases. It is now also recognized that many IDPs remain dynamic even in specific complexes and functional assemblies. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for a mechanistic understanding of IDPs in biology, diseases, and therapeutics. Here, we provide an in-depth review of recent advances in the multi-scale simulation of disordered protein states, with a particular emphasis on the development and application of advanced sampling techniques for studying IDPs. These techniques are critical for adequate sampling of the manifold functionally relevant conformational spaces of IDPs. Together with dramatically improved protein force fields, these advanced simulation approaches have achieved substantial success and demonstrated significant promise towards the quantitative and predictive modeling of IDPs and their dynamic interactions. We will also discuss important challenges remaining in the atomistic simulation of larger systems and how various coarse-grained approaches may help to bridge the remaining gaps in the accessible time- and length-scales of IDP simulations.

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

We have performed multicanonical molecular dynamics (McMD) based dynamic docking simulations to study and compare the binding mechanism between two medium-sized inhibitors (ABT-737 and WEHI-539) that bind to the cryptic site of Bcl-xL, by exhaustively sampling the conformational and configurational space. Cryptic sites are binding pockets that are transiently formed in the apo state or are induced upon ligand binding. Bcl-xL, a pro-survival protein involved in cancer progression, is known to have a cryptic site, whereby the shape of the pocket depends on which ligand is bound to it. Starting from the apo-structure, we have performed two independent McMD-based dynamic docking simulations for each ligand, and were able to obtain near-native complex structures in both cases. In addition, we have also studied their interactions along their respective binding pathways by using path sampling simulations, which showed that the ligands form stable binding configurations via predominantly hydrophobic interactions. Although the protein started from the apo state, both ligands modulated the pocket in different ways, shifting the conformational preference of the sub-pockets of Bcl-xL. We demonstrate that McMD-based dynamic docking is a powerful tool that can be effectively used to study binding mechanisms involving a cryptic site, where ligand binding requires a large conformational change in the protein to occur.

Key Factors in Conformation Transformation of an Important Neuronic Protein Glucose Transport 3 Revealed by Molecular Dynamics Simulation

Glucose transporters (GLUTs) are an essential kind of protein that exists in the neuron and are responsible for glucose transport. In the present study, we performed molecular dynamic simulations to deeply understand the glucose uptake mechanism. According to our results, we reconstruct the glucose uptake model of the GLUT3, which is similar to the working model of GLUTs raised by Yan et al., and find a new intermediate state ( Yan, N., et al. ( 2015 ) Molecular basis of ligand recognition and transport by glucose transporters , Nature 526 , 391 - 396 ). In addition, we discover the bottleneck residues for the protein conformational switch. Water molecules are also important for the conformational switch by influencing the hydrogen bond networks of the glucose-protein complex, which can cause the obvious rearrangement of corresponding transmembrane segments. Our findings may shed light on the glucose uptake process of this key neuronic transmembrane protein and the functional relationships between the multiple intermediate states.

In vitro modulation of mercury-induced rat liver mitochondria dysfunction

Mercury (Hg) is a toxic environmental pollutant that exerts its cytotoxic effects as cations by targeting mitochondria. In our work, we determined different mitochondrial toxicity factors using specific substrates and inhibitors following the addition of Hg2+ to the mitochondria isolated from Wistar rat liver in vitro. We found that Hg2+ induced marked changes in the mitochondrial ultrastructure accompanied by mitochondrial swelling, mitochondrial membrane potential collapse, mitochondrial membrane fluidity increase and Cytochrome c release. Additionally, the effects of Hg2+ on heat production of mitochondria were investigated using microcalorimetry; simultaneously, the effects on mitochondrial respiration were determined by Clark oxygen-electric methods. Microcalorimetry could provide detailed kinetic and thermodynamic information which demonstrated that Hg2+ had some biotoxicity effect on mitochondria. The inhibition of energy metabolic activities suggested that high concentrations of Hg2+ could induce mitochondrial ATP depletion under MPT and mitochondrial respiration inhibition. These results help us learn more about the toxicity of Hg2+ at the subcellular level.

Mitochondrial toxicity induced by a thiourea gold(i) complex: mitochondrial permeability transition and respiratory deficit

Gold(i) complexes have been widely used as antibacterial and antitumor agents because of their excellent biological activities. However, there are few reports on the study of gold(i) complexes at the subcellular level. Herein, we investigated the toxicity of a gold(i) complex (N,N'-disubstituted cyclic thiourea ligand) - AuTuCl - to isolated mitochondria via various methods. The results showed that AuTuCl induced mitochondrial swelling, elevated ROS generation and triggered collapse of the membrane potential, which indicated the induction of mitochondrial permeability transition (MPT). It also enhanced the permeability of H+ and K+ of the inner membrane and declined membrane fluidity, which might be the result of MPT. Moreover, AuTuCl impaired the mitochondrial respiratory chain and suppressed the activities of complexes II and IV in the respiratory chain. It also triggered the deficiency of ATP and the effusion of Cyt c, which were strictly related to respiration and apoptosis. These results indicated that AuTuCl severely affected the structure and function of mitochondria. It was proposed that MPT and impairment of the respiratory chain were responsible for the mitotoxicity of AuTuCl, thus causing energy deficiency and even apoptosis. This conceivable mechanism can serve as a clue for better understanding of the toxicology of AuTuCl.

Surface functional groups affect CdTe QDs behavior at mitochondrial level

Quantum dots (QDs) are used in the bio-medical area because of their excellent optical properties. Their biomedical utilization has remained a serious biosecurity concern. Cytotoxicity experiments have shown that QD toxicity is connected to the properties of the QDs. In this paper, the toxicity of QDs was studied from the aspect of surface functional groups at the mitochondrial level. Three types of ligands, thioglycollic acid (TGA), mercaptoethylamine (MEA) and l-cysteine (l-Cys), which have similar structures but different functional groups were used to coat CdTe QDs. The effects of the three types of CdTe QDs on mitochondria were then observed. The experimental results showed the three types of CdTe QDs could impair mitochondrial respiration, destroy membrane potential and induce mitochondrial swelling. Interestingly, MEA-CdTe QDs showed similar effects on membrane potential and mitochondrial swelling as did l-Cys-CdTe QDs, while TGA-CdTe QDs showed stronger effects than that of the two other QDs. Moreover, the three types of CdTe QDs showed significantly different effects on mitochondrial membrane fluidity. MEA-CdTe QDs decreased mitochondrial membrane fluidity, l-Cys-CdTe QDs showed no obvious influence on mitochondrial membrane fluidity and TGA-CdTe QDs increased mitochondrial membrane fluidity. The interaction mechanism of CdTe QDs on mitochondrial permeability transition (MPT) pores as well as Cd²⁺ release by CdTe QDs were checked to determine the reason for their different effects on mitochondria. The results showed that the impact of the three types of CdTe QDs on mitochondria was not only related to the released metal ion, but also to their interaction with MPT pore proteins. This work emphasizes the importance of surface functional groups in the behavior of CdTe QDs at the sub-cellular level.

Mitochondrial morphology and function impaired by dimethyl sulfoxide and dimethyl Formamide

In this work, the effects of two non-ionic, non-hydroxyl organic solvents, dimethyl sulfoxide (DMSO) and dimethyl formamide (DMF) on the morphology and function of isolated rat hepatic mitochondria were investigated and compared. Mitochondrial ultrastructures impaired by DMSO and DMF were clearly observed by transmission electron microscopy. Spectroscopic and polarographic results demonstrated that organic solvents induced mitochondrial swelling, enhanced the permeation to H⁺/K⁺, collapsed the potential inner mitochondrial membrane (IMM), and increased the IMM fluidity. Moreover, with organic solvents addition, the outer mitochondrial membrane (OMM) was broken, accompanied with the release of Cytochrome c, which could activate cell apoptosis signaling pathway. The role of DMSO and DMF in enhancing permeation or transient water pore formation in the mitochondrial phospholipid bilayer might be the main reason for the mitochondrial morphology and function impaired. Mitochondrial dysfunctions induced by the two organic solvents were dose-dependent, but the extents varied. Ethanol (EtOH) showed the highest potential damage on the mitochondrial morphology and functions, followed by DMF and DMSO.

The interactions of CdTe quantum dots with serum albumin and subsequent cytotoxicity: the influence of homologous ligands

With spreading applications of fluorescent quantum dots (QDs) in biomedical fields in recent years, there is increasing concern over their toxicity. Among various factors, surface ligands play critical roles. Previous studies usually employed QDs with different kinds of surface ligands, but general principles were difficult to be obtained since it was hard to compare these surface ligands with varied chemical structures without common features. Herein, the physicochemical properties of two types of CdTe QDs were kept very similar, but different in the surface ligands with mercaptoacetic acid (TGA) and 3-mercaptopropionic acid (MPA), respectively. These two types of homologous ligands only had a difference in one methylene group (-CH2-). The interactions of the two types of CdTe QDs with bovine serum albumin (BSA), which was one of the main components of cell culture, were studied by fluorescence, UV-vis absorption, and circular dichroism spectroscopy. It was found that the fluorescence quenching of BSA by CdTe QDs followed a static quenching mechanism, and there was no obvious difference in the Stern-Volmer quenching constants and binding constants. The thermodynamic parameters of the two types of QDs were similar. BSA underwent conformational changes upon association with these QDs. By comparing the cytotoxicity of these two types of QDs, TGA-capped QDs were found to be less cytotoxic than MPA-capped QDs. Besides, in the presence of serum proteins, the cytotoxicity of the QDs was reduced. QDs in the absence of serum proteins had a higher internalization efficiency, compared with those in the medium with serum. To the best of our knowledge, this is a rare study focusing on surface ligands with such small variations at the biomolecular and cellular levels. These findings can provide new insights for the design and applications of QDs in complex biological media.