Advancing structural biology through breakthroughs in AI

The past century has witnessed an exponential increase in our atomic-level understanding of molecular and cellular mechanisms from a structural perspective, with multiple landmark achievements contributing to the field. This, coupled with recent and continuing breakthroughs in artificial intelligence methods such as AlphaFold2, and enhanced computational power, is enabling our understanding of protein structure and function at unprecedented levels of accuracy and predictivity. Here, we describe some of the major recent advances across these fields, and describe, as these technologies coalesce, the potential to utilise our enhanced knowledge of intricate cellular and molecular systems to discover novel therapeutics to alleviate human suffering.     

The long coming of computational structural biology

Fifty years ago, the structures of the alpha-helix, the beta-sheet, the alpha-helical coiled coil and the collagen triple helix raised the expectation that protein structure could be understood computationally, using a combination of geometric considerations, model-building and parametric equations. The first crystal structures dispelled this hope, revealing a disconcerting lack of regularity in the folding patterns of proteins. Gradually it became clear that the protein folding problem-namely deducing the structure of a protein from its amino acid sequence-was of exceptional difficulty. Its solution has remained outside our reach to this day and, arguably, it represents the most important unsolved problem in molecular biology. Nevertheless, our ability to understand and predict molecular structure by computational means has made steady progress, suggesting that we will eventually conquer the problem, not by a few heroic insights, but by steady advances in biophysical knowledge, biological databases, software applications and raw computer power. Computational structural biology, whose influence is already pervasive, will come to dominate structural approaches in the next decades.     

Recent applications of Hidden Markov Models in computational biology

This paper examines recent developments and applications of Hidden Markov Models (HMMs) to various problems in computational biology, including multiple sequence alignment, homology detection, protein sequences classification, and genomic annotation.     

Recent progress in the biology, chemistry and structural biology of DNA glycosylases

Since the discovery in 1974 of uracil DNA glycosylase (UDG), the first member of the family of enzymes involved in base excision repair (BER), considerable progress has been made in the understanding of DNA glycosylases, the polypeptides that remove damaged or mispaired DNA bases from DNA. We also know the enzymes that act downstream of the glycosylases, in the processing of abasic sites, in gap filling and in DNA ligation. This article covers the most recent developments in our understanding of BER, with particular emphasis on the mechanistic aspects of this process, which have been made possible by the elucidation of the crystal structures of several glycosylases in complex with their respective substrates, substrate analogues and products. The biological importance of individual BER pathways is also being appreciated through the inactivation of key BER genes in knockout mouse models.     

Recent advances in the structural biology of the 26S proteasome

There is growing appreciation for the fundamental role of structural dynamics in the function of macromolecules. In particular, the 26S proteasome, responsible for selective protein degradation in an ATP dependent manner, exhibits dynamic conformational changes that enable substrate processing. Recent cryo-electron microscopy (cryo-EM) work has revealed the conformational dynamics of the 26S proteasome and established the function of the different conformational states. Technological advances such as direct electron detectors and image processing algorithms allowed resolving the structure of the proteasome at atomic resolution. Here we will review those studies and discuss their contribution to our understanding of proteasome function.     

Recent advances in the structural biology of chondroitin sulfate and dermatan sulfate

Recent glycobiology studies have suggested fundamental biological functions for chondroitin, chondroitin sulfate and dermatan sulfate, which are widely distributed as glycosaminoglycan sidechains of proteoglycans in the extracellular matrix and at cell surfaces. They have been implicated in the signaling functions of various heparin-binding growth factors and chemokines, and play critical roles in the development of the central nervous system. They also function as receptors for various pathogens. These functions are closely associated with the sulfation patterns of the glycosaminoglycan chains. Surprisingly, nonsulfated chondroitin is indispensable in the morphogenesis and cell division of Caenorhabditis elegans, as revealed by RNA interference experiments of the recently cloned chondroitin synthase gene and by the analysis of mutants of squashed vulva genes.     

Recent breakthroughs in the study of salicylic acid biosynthesis

Salicylic acid is an important regulator of induced plant resistance to pathogens. Consequently, the biosynthesis of salicylic acid and its regulation has received a lot of attention. Salicylic acid can be made from phenylalanine via cinnamic and benzoic acid. Recently, genetic studies in Arabidopsis have shown that salicylic acid is made in the chloroplast from isochorismate, a pathway that is known to operate in prokaryotes.     

Recent advances in small-angle scattering and its expanding impact in structural biology

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Recent advances in the structural biology of modular polyketide synthases and nonribosomal peptide synthetases

Polyketides and nonribosomal peptides are an important class of natural products with useful bioactivities. These compounds are similarly biosynthesized using enzymes with modular structures despite having different physicochemical properties. These enzymes are attractive targets for bioengineering to produce “unnatural” natural products owing to their modular structures. Therefore, their structures have been studied for a long time; however, the main focus was on truncated-single domains. Surprisingly, there is an increasing number of the structures of whole modules reported, most of which have been enabled through the recent advances in cryogenic electron microscopy technology. In this review, we have summarized the recent advances in the structural elucidation of whole modules.