A Molecular Dynamics Perspective To Identify Precursors to Aggregation in Human γS-Crystallin Unravels the Mechanism of Childhood Cataracts

A bibliometric and visualized analysis of the pathogenesis of cataracts from 1999 to 2023

Research on the pathogenesis of cataracts is ongoing and the number of publications on this topic is increasing annually. This study offers an overview of the research status, popular topics, and scholarly tendencies in the field of cataract pathogenesis over recent decades，which helps to guide future research directions, and optimize resource allocation. In the present study, we performed a bibliometric analysis of cataract pathogenesis. Publications from January 1, 1999, to December 20, 2023, were collected from the Web of Science Core Collection (WoSCC), and the extracted data were quantified and analyzed. We analyzed and presented the data using Microsoft Excel, VOSviewer, CiteSpace, and Python. In all, 4006 articles were evaluated based on various characteristics, including publication year, authors, countries, institutions, journals, citations, and keywords. This study utilized VOSviewer to conduct visualized analysis, including co-authorship, co-citation, co-occurrence, and network visualization. The CiteSpace software was used to identify keywords with significant bursts of activity. The number of annual global publications climbed from 76 to 277 between 1999 and 2023, a 264.47% rise. Experimental Eye Research published the most manuscripts (178 publications), whereas Investigative Ophthalmology & Visual Science received the most citations (6675 citations). The most influential and productive country, institution, and author were the United States (1244 publications, 54,456 citations), University of California system (136 publications, 5401 citations), and Yao Ke (49 publications, 838 citations), respectively. The top 100 ranked keywords are divided into four clusters through co-occurrence analysis: (1) secondary cataracts, (2) oxidative stress, (3) gene mutations and protein abnormalities, and (4) alteration of biological processes in lens epithelial cells. Further discussions on the four subtopics outline the research topics and trends. In conclusion, the specific mechanism of cataract formation remains a popular topic for future research and should be explored in greater depth.

Effect of mutations on the folding and stability of γD-crystallin protein

Interprotein interactions between the partially unfolded states of γD-crystallin (γD-crys) protein are known to cause cataracts. Therefore, understanding the unfolding pathways of native γD-crys is extremely crucial to delineate their aggregation mechanism. In this study, we have performed extensive all-atom Molecular Dynamics simulations with explicit solvent to understand the role of the critical residues that drive the stability of the motifs and domains of γD-crys in its wild type and mutant forms. Our findings show that while the individual motifs of wild type are not stable in the native form, the individual domains remain structurally stable at 425K. This enhanced stability of the domain was attributed to the hydrophobic interactions between the motifs. Single and double point mutations of the domains with negatively charged aspartic and glutamic acid amino acid residues (I3E, W42D, W42E, I3D/W42D, I3E/W42E, and L92D/W157D) decreases the structural stability, leading to unfolding of individual domains of γD-crys. We believe that our study sheds light on the weakest links of γD-crys, along with the role of interactions stabilizing the domains. Further, this study bolsters and provides a better understanding of the domain swapping mechanism of aggregation of γD-crys.Communicated by Ramaswamy H. Sarma.

Acquired disorder and asymmetry in a domain-swapped model for γ-crystallin aggregation

Misfolding and aggregation of proteins occur in many pathological states. Because of the inherent disorder involved, these processes are difficult to study. We attempted to capture aggregation intermediates of γ S-crystallin, a highly stable, internally symmetrical monomeric protein, by crystallization under mildly acidic and oxidizing conditions. Here we describe novel oligomerization through strained domain-swapping and partial intermolecular disulfide formation. This forms an octamer built from asymmetric tetramers, each of which comprises an asymmetric pair of twisted, domain-swapped dimers. Each tetramer shows patterns of acquired disorder among subunits, ranging from local loss of secondary structure to regions of intrinsic disorder. The octamer ring is tied together by partial intermolecular disulfide bonds, which may contribute to strain and disorder in the octamer. Oligomerization in this structure is self-limited by the distorted octamer ring. In a more heterogeneous environment, the disordered regions could serve as seeds for cascading interactions with other proteins. Indeed, solubilized protein from crystals retain many features observed in the crystal and are prone to further oligomerization and precipitation. This structure illustrates modes of loss of organized structure and aggregation that are relevant for cataract and for other disorders involving deposition of formerly well-folded proteins.

Fundamental Challenges and Outlook in Simulating Liquid-Liquid Phase Separation of Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) populate an ensemble of dynamic conformations, making their structural characterization by experiments challenging. Many IDPs undergo liquid-liquid phase separation into dense membraneless organelles with myriad cellular functions. Multivalent interactions in low-complexity IDPs promote the formation of these subcellular coacervates. While solution NMR, Förster resonance energy transfer (FRET), and small-angle X-ray scattering (SAXS) studies on IDPs have their own challenges, recent computational methods draw a rational trade-off to characterize the driving forces underlying phase separation. In this Perspective, we critically evaluate the scope of approximation-free field theoretic simulations, well-tempered ensemble methods, enhanced sampling techniques, coarse-grained force fields, and slab simulation approaches to offer an improved understanding of phase separation. A synergy between simulation length scale and model resolution would reduce the existing caveats and enable theories of polymer physics to elucidate finer details of liquid-liquid phase separation (LLPS). These computational advances offer promise for rigorous characterization of the IDP proteome and designing peptides with tunable material and self-assembly properties.

Exploring the folding process of human βB2-crystallin using multiscale molecular dynamics and the Markov state model

Adequate knowledge of protein conformations is crucial for understanding their function and their association properties with other proteins. The cataract disease is correlated with conformational changes in key proteins called crystallins. These changes are due to mutations or post-translational modifications that may lead to protein unfolding, and thus the formation of aggregate states. Human βB2-crystallin (HβB2C) is found in high proportion in the eye lens, and its mutations are related to some cataracts. HβB2C also associates into dimers, tetramers, and other higher-order supramolecular complexes. However, it is the only protein of the βγ-crystallin family that has been found in an extended conformation. Therefore, we hypothesize that the extended conformation is not energetically favourable and that HβB2C may adopt a closed (completely folded) conformation, similar to the other members of the βγ-crystallin family. To corroborate this hypothesis, we performed extensive molecular dynamics simulations of HβB2C in its monomeric and dimeric conformations, using all-atom and coarse-grained scales. We employed Markov state model (MSM) analysis to characterize the conformational and kinetically relevant states in the folding process of monomeric HβB2C. The MSM analysis clearly shows that HβB2C adopts a completely folded structure, and this conformation is the most kinetically and energetically favourable one. In contrast, the extended conformations are kinetically unstable and energetically unfavourable. Our MSM analysis also reveals a key metastable state, which is particularly interesting because it is from this state that the folded state is reached. The folded state is stabilized by the formation of two salt bridges between the residue-pairs E74-R187 and R97-E166 and the two hydrophobic residue-pairs V59-L164 and V72-V151. Furthermore, free energy surface (FES) analysis revealed that the HβB2C dimer with both monomers in a closed conformation (face-en-face dimer) is energetically more stable than the domain-swapped dimer (crystallographic structure). The results presented in this report shed light on the molecular details of the folding mechanism of HβB2C in an aqueous environment and may contribute to interpreting different experimental findings. Finally, a detailed knowledge of HβB2C folding may be key to the rational design of potential molecules to treat cataract disease.

A Perspective on Biophysical Studies of Crystallin Aggregation and Implications for Cataract Formation

Lens crystallins are subject to various types of damage during their lifetime which triggers protein misfolding and aggregation, ultimately causing cataracts. There are several models for crystallin aggregation, but a comprehensive picture of the mechanism of cataract is still underway. The complex biomolecular interactions underlying crystallin aggregation have motivated major efforts to resolve the structural details and mechanism of aggregation using multiple biophysical techniques at different resolutions. Together, experimental and computational approaches identify and characterize both amyloidogenic and amorphous aggregates leading to an improved understanding of crystallin aggregation. A rigorous characterization of the aggregation-prone intermediates is crucial in cataract-mediated drug discovery. This Perspective summarizes recent biophysical studies on lens crystallin aggregation. We evaluate the outstanding challenges, future outlook, and rewards in this fertile field of research. With lessons learned from protein folding and multiple pathways of aggregation, we highlight the differences in the overall mechanisms of age-related and congenital cataracts. We expect that a correlation between the existing and developing biophysical techniques would provide a platform to study amyloid architecture in the eye lens and reduce the existing gaps in our understanding of crystallin biophysics.