抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort1–4, the structures of around 100,000 unique proteins have been determined5, but this represents a small fraction of the billions of known protein sequences6,7. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’8—has been an important open research problem for more than 50 years9. Despite recent progress10–14, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14)15, demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.

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Highly accurate protein structure prediction with AlphaFold

Physical Biology of the Cell, 2nd Edition, is a textbook that focuses on the application of physical principles to understanding biological systems. The subject matter of the text is organized according to common physical principles that govern biological processes rather than in relation to the biological processes themselves, as is common for most biology and cell biology textbooks. Topics covered in the book span a broad range of interests, including electrostatics, molecular interactions, molecular motors and the cytoskeleton, and membranes. Each chapter features color figures, derived equations with relevant examples, and problem sets at the chapter’s conclusion. The problem sets at the end of the chapters are expanded from the first edition. Further, the second edition includes two new chapters, one on light and pattern formation, and another on the use of computation in exploring biological problems. Additional student and instructor resources are also available online.

The primary audience for the textbook could include advanced undergraduate students or first-year graduate students. While the textbook may be best suited for a biophysics course, it could also be used as a primary or supplementary text for teaching cellular and molecular biology. As a teaching tool for cellular and molecular biology, the many examples featured throughout the text could easily be employed to assist students in learning the principles of how a cellular or molecular system functions. A basic level of mathematical proficiency would be required of the student. While this textbook could be an excellent resource for many courses, there are several topics commonly covered in biochemistry classes, such the glycolytic pathway, that are featured in the book but in different contexts than many widely used biochemistry texts. For a biophysics course that is heavily focused on techniques, individual references that discuss the specific techniques in detail would be more suitable than this book. Of course, any instructor seeking to use this textbook should be aware of its content before making a selection.

This textbook is an excellent resource, both for a research scientist and for a teacher. The authors do a superb job of selecting the material for each chapter and explaining the material with equations and narrative in an easily digestible manner. Readers who enjoy this book may also enjoy Molecular Driving Forces by Dill and Bromberg, which gives excellent treatment of similar concepts.

Physical Biology of the Cell

The mechanism by which bacteria divide is not well understood. Cell division is mediated by filaments of FtsZ and FtsA (FtsAZ) that recruit septal peptidoglycan-synthesizing enzymes to the division site. To understand how these components coordinate to divide cells, we visualized their movements relative to the dynamics of cell wall synthesis during cytokinesis. We found that the division septum was built at discrete sites that moved around the division plane. FtsAZ filaments treadmilled circumferentially around the division ring and drove the motions of the peptidoglycan-synthesizing enzymes. The FtsZ treadmilling rate controlled both the rate of peptidoglycan synthesis and cell division. Thus, FtsZ treadmilling guides the progressive insertion of new cell wall by building increasingly smaller concentric rings of peptidoglycan to divide the cell.

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Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division

К пробиотикам относят «живые микроорганизмы, которые при введении в адекватных количествах оказывают положительное влияние на здоровье хозяина» [1]. В то время как применению некоторых из них (Lactobacillus, Bifidobacterium) было уделено много внимания, другие были изучены позже, и их важное лечебное действие становится ясным только сейчас. Одним из пробиотиков является грамположительная палочка Bacillus subtilis (B.subtilis). Большинство бактерий рода Bacillus (включая B.subtilis) не опасны для человека и широко распространены в окружающей среде. Их обнаруживают в почве, воде, воздухе и пищевых продуктах (пшеница, другие зерновые культуры, хлебобулочные изделия, соевые продукты, цельное мясо, сырое и пастеризованное молоко). Как следствие, они постоянно попадают в желудочно-кишечный тракт и дыхательные пути, засевая эти отделы. Количество бацилл в кишечнике может достигать 10 КОЕ/г, что сравнимо с аналогичным показателем у Lactobacillus. В связи с этим ряд исследователей рассматривают бактерии рода Bacillus как один из доминирующих компонентов нормальной микрофлоры кишечника [2]. В то же время лечебное введение B.subtilis позволяет использовать данный микроорганизм в качестве пробиотика по четырем основным направлениям: 1) для защиты от кишечных патогенов; 2) от дыхательных патогенов; 3) для устранения дисбактериоза при антибиотикотерапии; 4) для усиления переваривания и продвижения пищи. Упрощенная схема пробиотической активности B.subtilis при патологии желудочнокишечного тракта представлена на рис. 1. Таким образом, в научных работах последних десятилетий были сделаны значительные продвижения в выяснении спектра пробиотической активности B.subtilis, что делает данную бактерию одним из наиболее привлекательных пробиотиков для медицинского применения. В настоящем обзоре мы представляем данные соответствующих экспериментальных и клинических исследований, позволяющих составить впечатление о терапевтическом потенциале B.subtilis. УДК 615.331:579.852.1

Bacillus subtilis. (Book Reviews: The Molecular Biology of the Bacilli; Molecular Cloning and Gene Regulation in Bacilli)

Many bacteria are surrounded by both a cell membrane and a cell wall – a rigid outer covering made of sugars and short protein chains. The cell wall often determines which of a variety of shapes – such as rods or spheres – the bacteria grow into. One protein required to form the rod shape is called MreB. This protein forms filaments that bind to the bacteria’s cell membrane and associate with the enzymes that build the cell wall. Together, these filament-enzyme complexes rotate around the cell to build and reinforce the cell wall in a hoop-like manner. But how do the MreB filaments know how to move around the circumference of the rod, instead of moving in any other direction? Using a technique called total internal reflection microscopy to study how MreB filaments move across bacteria cells, Hussain, Wivagg et al. show that the filaments sense the shape of a bacterium by orienting along the direction of greatest curvature. As a result, the filaments in rod-shaped cells orient and move around the rod, while in spherical bacteria they move in all directions. However, spherical bacteria can regenerate into rods from small surface ‘bulges’. The MreB filaments in the bulges move in an oriented way, helping them to generate the rod shape. Hussain, Wivagg et al. also found that forcing cells that lack a cell wall into a rod shape caused the MreB filaments bound to the cell membrane to orient and circle around the rod. This shows that the organization of the filaments is sufficient to shape the cell wall. In the future, determining what factors control the activity of the MreB filaments and the enzymes they associate with might reveal new targets for antibiotics that disrupt the cell wall and so kill the bacteria. This will require higher resolution microscopes to be used to examine the cell wall in more detail. The activity of all the proteins involved in building cell walls will also need to be extensively characterized.

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MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis.

Peptidoglycan is an essential crosslinked polymer that surrounds bacteria and protects them from osmotic lysis. β-lactam antibiotics target the final stages of peptidoglycan biosynthesis by inhibiting the transpeptidases that crosslink glycan strands to complete cell wall assembly. Characterization of transpeptidases and their inhibition by β-lactams have been hampered by lack of access to a suitable substrate. We describe a general approach to accumulate Lipid II in bacteria and to obtain large quantities of this cell wall precursor. We demonstrate the utility of this strategy by isolating Staphylococcus aureus Lipid II and reconstituting the synthesis of crosslinked peptidoglycan by the essential penicillin-binding protein 2 (PBP2), which catalyzes both glycan polymerization and transpeptidation. We also show that we can compare the potencies of different β-lactams by directly monitoring transpeptidase inhibition. The methods reported here will enable a better understanding of cell wall biosynthesis and facilitate studies of next-generation transpeptidase inhibitors.

Lipid II overproduction allows direct assay of transpeptidase inhibition by β-lactams.

Penicillin-binding proteins (PBPs) are involved in the synthesis and remodeling of bacterial peptidoglycan (PG). Staphylococcus aureus expresses four PBPs. Genetic studies in S. aureus have implicated PBP4 in the formation of highly cross-linked PG, but biochemical studies have not reached a consensus on its primary enzymatic activity. Using synthetic Lipid II, we show here that PBP4 preferentially acts as a transpeptidase (TP) in vitro. Moreover, it is the PBP primarily responsible for incorporating exogenous d-amino acids into cellular PG, implying that it also has TP activity in vivo. Notably, PBP4 efficiently exchanges d-amino acids not only into PG polymers but also into the PG monomers Lipid I and Lipid II. This is the first demonstration that any TP domain of a PBP can activate the PG monomer building blocks. Exploiting the promiscuous TP activity of PBP4, we developed a simple, highly sensitive assay to detect cellular pools of lipid-linked PG precursors, which are of notoriously low abundance. Th...

/pdf/detection-of-lipid-linked-peptidoglycan-precursors-by-24zeg33t1r.pdf

Detection of lipid-linked peptidoglycan precursors by exploiting an unexpected transpeptidase reaction.

Lysobactin, also known as katanosin B, is a potent antibiotic with in vivo efficacy against Staphylococcus aureus and Streptococcus pneumoniae. It was previously shown to inhibit peptidoglycan (PG) biosynthesis, but its molecular mechanism of action has not been established. Using enzyme inhibition assays, we show that lysobactin forms 1:1 complexes with Lipid I, Lipid II, and Lipid IIAWTA, substrates in the PG and wall teichoic acid (WTA) biosynthetic pathways. Therefore, lysobactin, like ramoplanin and teixobactin, recognizes the reducing end of lipid-linked cell wall precursors. We show that despite its ability to bind precursors from different pathways, lysobactin’s cellular mechanism of killing is due exclusively to Lipid II binding, which causes septal defects and catastrophic cell envelope damage.

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The Mechanism of Action of Lysobactin.

Sacculus is a peptidoglycan (PG) matrix that protects bacteria from osmotic lysis. In Gram-positive organisms, the sacculus is densely functionalized with glycopolymers important for survival, but the way in which assembly occurs is not known. In Staphylococcus aureus, three LCP (LytR-CpsA-Psr) family members have been implicated in attaching the major glycopolymer wall teichoic acid (WTA) to PG, but ligase activity has not been demonstrated for these or any other LCP proteins. Using WTA and PG substrates produced chemoenzymatically, we show that all three proteins can transfer WTA precursors to nascent PGs, establishing that LCP proteins are PG-glycopolymer ligases. Although all S. aureus LCP proteins have the capacity to attach WTA to PG, we show that their cellular functions are not redundant. Strains lacking lcpA have phenotypes similar to those of WTA-null strains, indicating that this is the most important WTA ligase. This work provides a foundation for studying how LCP enzymes participate in cell wall assembly.

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Kaitlin Schaefer

Papers

MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis.

Lipid II overproduction allows direct assay of transpeptidase inhibition by β-lactams.

Detection of lipid-linked peptidoglycan precursors by exploiting an unexpected transpeptidase reaction.

The Mechanism of Action of Lysobactin.

In vitro reconstitution demonstrates the cell wall ligase activity of LCP proteins