Structural Molecular Biology

Illuminating Biological Structures at the Atomic and Molecular Levels

Science Highlights


  • The Solution Structural Ensembles of RNA and RNA·Protein Complexes

    RNAs play many functional roles in biology, from non-coding RNAs directly regulating gene expressions to structured RNAs acting as molecular machines essential to chromosome maintenance, alternative pre-mRNA splicing, protein synthesis, and protein export. RNA function typically involves a series of conformational steps, which can be considered as different conformational states that can be adopted by the same RNA.

  • Structure of the Cell’s DNA Gatekeeper

    The nuclear pore complex (NPC), a very large macromolecular machine embedded in the nuclear envelope, is the sole gateway for the bi-directional transport of macromolecules between the nucleus and cytoplasm. The NPC is also involved in diverse cellular processes, including transcription, mRNA maturation, and genome organization.

  • A New Type of Pilus from the Human Microbiome

    Pili (or fimbriae) are hair-like structures on the cell surface of many bacteria. Pili can play a variety of functions in bacteria, such as conjugation, mobility and adhesion, and often serve as primary virulence factors. Pili are formed by noncovalent or covalent oligomerization of component proteins, pilins or fimbrilins.

  • Structure, Inhibition and Regulation of Two-pore Channel TPC1 from Arabidopsis thaliana

    Using macromolecular crystallography beam lines at SSRL and the ALS scientists Alexander F. Kintzer and Robert M. Stroud at the University of California, San Francisco (UCSF) determined the structure of the first intracellular, voltage-gated, transmembrane protein ion channel, called two-pore channel 1 or TPC1, with an allosteric inhibitor Ned-19 bound to the outside of the channel.

  • Discovery of Next Generation RAF Inhibitors that Dissociate Paradoxical Activation from Inhibition of the MAPK Pathway

    Genes encoding members of the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathway are frequently mutated in human cancer. RAS (a small GTPase) and RAF (a serine/Threonine kinase) are two major nodes on this important signaling axis. Constitutive activation of BRAF, a member of the RAF family, has been shown to promote RAS independent MAPK pathway up-regulation1.

  • Revealing a New Conformational State in a Chloride/Proton Exchanger

    “CLC” transporters are secondary active-transport membrane proteins that catalyze the transmembrane exchange of chloride (Cl-) for protons (H+). This exchange plays an essential role in proper cardiovascular, neuronal, muscular and epithelial functions. Several diseases arise from CLC defects, and several CLCs are therapeutic targets.

  • 2015

  • Translocator Protein Structure and Function

    Translocator protein (TSPO) is an ancient conserved protein whose functions in bacteria and higher eukaryotes are yet to be clearly defined in spite of more than 30 years of study. In mitochondria, it was first recognized as an outer membrane protein that binds benzodiazepine drugs, but distinct from the central nervous system site, the GABAA receptor.

  • Crystal Structures of the Synaptotagmin-SNARE Complex that is Essential for Synchronous Synaptic Neurotransmitter Release

    Scientists at Stanford University School of Medicine have determined the 3-D structure of a complex of synaptic proteins that controls the release of signaling chemicals (called neurotransmitters, such as glutamate, dopamine or serotonin) from brain cells in less than one-thousandth of a second, which ultimately could help unlock a new realm of drug research targeting brain disorders.

  • Significantly Shorter Fe–S Bond in Cytochrome P450-I is Consistent with Greater Reactivity Relative to Chloroperoxidase

    C-H bond activation is often considered the “holy grail” of inorganic chemists, as the ability to specifically activate C-H bonds would be one of the most used transformations in all of chemistry. Cytochrome P450s (P450s) are thiolate ligated heme proteins that are often referred to as nature’s detoxifiers and can do this difficult C-H bond activation with ease. P450s are known to hydroxylate C-H bonds on the order of about 98-100 kcal/mol.

  • Discovery of the Fundamental Mechanism of Action of Resveratrol

    Resveratrol is reported to extend lifespan and provide cardio-neuro-protective, anti-diabetic, and anti-cancer effects by initiating a protective stress response. Resveratrol is produced in grapes, cacao beans (dark chocolates), peanuts (peanut butter), Japanese knotweed, blueberries and some other plants, in response to environmental stress conditions including infection, drought and ultraviolet radiation.

  • A Designed Supramolecular Protein Assembly with in-Vivo Enzymatic Activity

    A major goal in molecular design and engineering is the creation of new enzymes from scratch. However, the design of 3-dimensional protein architectures from first principles represents a formidable challenge, and as a result, the generation of new enzymatic activities has primarily relied on repurposing the interiors of pre-existing protein folds such as TIM barrels and αβ-hydrolases.

  • Reversible CO-binding to the Active Site of Nitrogenase

    All living organisms depend on the availability of nitrogen for incorporation into the basic biological building blocks such as amino acids and DNA. Globally the largest reservoir for nitrogen is the atmosphere, with an N2 content of roughly 78%. However, as a highly unreactive gas, most organisms are unable to directly utilize dinitrogen due to the severe energy barrier required to break the N-N-triple bond.

  • CRISPR RNA-guided Surveillance in Escherichia Coli

    Viruses that infect bacteria and archaea are the most abundant biological entities on the planet1. To defend themselves against these pervasive viral predators, bacteria have evolved sophisticated adaptive immune systems that rely on a repetitive chromosomal locus called CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat). Each CRISPR locus consists of short (30-40nt) repeats that are separated by viral or plasmid derived spacer sequences of about the same length.

  • Crystal Structure of Cascade

    Immune pathways protect all organisms from infection by genetic invaders such as viruses. It was recently discovered that prokaryotes protect against invasion by bacteriophages via an RNA based adaptive immune system, called the CRISPR system. By acting as a barrier to the exchange of genetic information, a major route for the acquisition of antibiotic-resistance and virulence factors, the CRISPR system modulates the evolution of pathogenic bacteria.

  • 2014

  • Antibody Recognition of the Influenza Hemagglutinin by Receptor Mimicry

    There has been a long-standing interest in blocking agents against influenza entry, such as inhibitors that can target the receptor binding site on the hemagglutinin surface glycoprotein (HA) to prevent viral attachment to host cells. Molecules have been designed based on the sialic acid receptor, although with very little success since sialic acid only has millimolar affinity to the HA.

  • New Method Tracks Metal-ion Movement in Periplasmic Proteins

    Copper is an essential nutrient for most organisms. However, it is toxic at high concentrations and, in fact, is used by macrophages to kill invading microbes. To counter the lethal effects of both environmental and host-defense onslaught, bacteria have devolved intricate efflux systems that impart full copper resistance.

  • A New Link between Human and Bacterial Signaling Machineries

    The human immune system relies on a network of protein sensors poised to detect foreign bacteria and viral pathogens. Researchers have discovered several families of receptors to explain how cells detect different types of microorganisms, but the evolutionary origin and specific signaling mechanism of these receptors often remain unclear.

  • Architectures of Whole-module and Bimodular Proteins from 6-Deoxyerythronolide B Synthase

    Secondary metabolites produced by microorganisms have a market value of over $30 billion annually, and nearly half of these compounds are naturally produced by bacteria in the phylum Actinobacteria. Phylum is a taxonomic rank in biology. It is below kingdom (e.g. Animal, Plant, Fungi etc.) and above class (e.g. Mammalia). Although there are over a dozen classes of secondary metabolites, the polyketides are arguably the most versatile with medically relevant activities including antibiotic, anticancer, immunosuppressive, anti-parasitic, and cholesterol-lowering properties.

  • Iron(IV)hydroxide pKa and the Role of Thiolate Ligation in C-H Bond Activation by Cytochrome P450

    Cytochrome P450s (P450s) are a family of monooxygenase enzymes that are nearly ubiquitous in nature. P450s are often described as biological blowtorches due to their incredible oxidizing power: They can hydroxylate C-H bonds of about 98-100 kcal/mol. P450s are responsible for the phase I metabolism of 75% of all pharmaceuticals in vivo and are thusly referred to as nature’s detoxifier.

  • Deconstructing the Peptide-MHC Specificity of T Cell Recognition

    T cells are tasked with detecting and counteracting infection and cellular dysfunction within an organism. Each T cell expresses a unique T-cell receptor (TCR), which is selected during T-cell development to bind to major histocompatibility complexes (MHCs) that display short (~8-15 amino acid) linear peptide antigens.

  • Fatty Acid Biosynthesis Caught in the Act

    The Escherichia coli (E. coli) proteome consists of 5993 proteins, of which 853 are involved in primary metabolic processes critical for the survival and functioning of the cell1. Fatty acid biosynthesis is at the core of primary metabolism responsible for the synthesis of fatty acids, essential metabolites that are the major components of cellular membranes and energy storage.

  • 2013

  • Structure of Chinese Herbal-based Medicine Captured by ATP on a Human tRNA Synthetase

    For approximately 2,000 years, the Chinese have been using the Chang Shan herb to treat malaria-induced fevers. A derivative of the herb's active ingredient has also been utilized in clinical trials for cancer and other therapies. Previous studies showed that the derivative, called halofuginone (HF), binds to an enzyme known as prolyl-tRNA synthetase (ProRS). Inhibition of ProRS by HF requires the additional presence of adenosine triphosphate (ATP), interestingly one of ProRS's three native substrates. Recent studies have shed new light on the structural interplay of ProRS, HF and ATP.

  • Structure of Human Argonaute2: A Programmable Ribonuclease

    Argonaute proteins play an important role in the biological process of RNA interference (RNAi). Scientists have now determined the crystal structure of human Argonaute2, thereby making progress toward a detailed understanding of Ago2 interactions with target RNA which may benefit the design of novel RNAi therapeutics.

  • Structure of the DUF2233 Domain in Bacteria and the Stuttering-associated UCE Glycoprotein

    UCE plays a key role in the functioning of lysosomes, cellular sacs full of digestive enzymes that break down bacteria, viruses and worn-out cell parts for recycling. When this recycling process goes awry, it can cause rare metabolic diseases such as Tay-Sachs and Gaucher, which often cause death in affected children by their early teens. Three years ago, researchers discovered that three mutations in UCE itself were linked to persistent stuttering that is passed down in families.

  • The Long-Sought Structure of a-Catenin Defines Its Functions for Cell-Cell Interactions

    Cells bind each other using specialized cell surface adhesion complexes called adherens junctions. These complexes direct the formation of tight, Velcro-like contacts that are essential for the development, architecture, maintenance, and function of tissues in all higher organisms. Exactly how this cell to cell binding is accomplished has not been fully understood. Researchers from the Florida campus of The Scripps Research Institute (TSRI) have now solved a piece of this puzzle by determining the structure of α-catenin using SSRL's Beam Line 11-1.

  • The Structure and Dynamics of Eukaryotic Glutaminyl-tRNA Synthetase

    Aminoacyl-tRNA synthetases are required in all three domains of life to add the correct amino acid to its cognate tRNA, an essential step in protein synthesis. Despite their importance, no structure had been reported for any full-length eukaryotic, glutaminyl-tRNA synthetase (GlnRS), although structural data for two prokaryotic GlnRS species exists.

  • Allosteric Activation and Modulation of Pentameric Ligand-gated Ion Channels

    Cys-loop receptors in eukaryotic cells control fast synaptic transmission and are important targets for various therapeutics which include general anesthetics. Although technical challenges have limited the determination of high-resolution structures for Cys-loop receptors, researchers from the University of Pittsburgh School of Medicine have taken advantage of two homologous proteins: the pentameric ligand-gated ion channels (pLGICs) found in the bacterium Erwinia chrysanthemi (ELIC) and the cyanobacterium Gloebacter violaceus (GLIC). The researchers carried out crystallographic studies of these pLGICs on SSRL Beam Line 12-2, investigating the structural underpinnings of the pLGIC activation process and the structural basis of anesthetic modulation of pLGICs.

  • Systematic Expansion of Porous Crystals to Include Large Molecules

    Recently, scientists at the University of California, Berkeley and Lawrence Berkeley National Laboratory and their collaborators synthesized a series of metal-organic frameworks (MOFs) with pores up to 98 Å in diameter—large enough to house protein molecules. For the first time the researchers were able to design strategies to overcome three major obstacles to increasing pore capacity...

  • The Lassa Virus Nucleoprotein Appears to Exhibit Conformational Control of Genome Binding

    Lassa virus is endemic in Western Africa, and is the most common cause of viral hemorrhagic fever, infecting an estimated 300,000-500,000 people annually. It is also the hemorrhagic fever most frequently transported out of Africa to the United States and Europe. Understanding the key proteins of Lassa virus and any Achilles' Heels written into their protein structures will enable development of therapeutics for medical defense. Recent analysis of the crystal structure of the virus' RNA binding domain done at SSRL may have revealed one promising area of vulnerability.

  • Structural Basis for Iron Piracy by Pathogenic Neisseria

    Of the 11 species of Neisseria bacteria that colonize humans, 9 of them coexist peacefully with us. However, two can cause serious diseases N. gonorrhoeae, responsible for the sexually transmitted disease gonorrhea, and N. meningitidis, which causes septicemia and meningitis. Commercially available vaccines exist for four of the five known disease-causing serogroups of N. meningitidis (A, B, C, Y, W135) but no vaccine exists to combat serogroup B (menB); nor is there a vaccine available against N. gonorrhoeae. One target for vaccine development against menB and N. gonorrhoeae is the iron transporters found on the pathogens' surfaces. Cut off their access to iron and these pathogens cannot survive.

  • 2012

  • Unusual Structure and Dynamics of an Artificial Enzyme Created in a Test Tube

    Until now this has been achieved only when extensive knowledge of the mechanism of the reaction is available. Recently, however, researchers have used a clever in vitro strategy to synthesize an artificial RNA ligase enzyme capable of a previously unknown catalytic activity, and to do so they began with a protein not associated with catalysis. A team of scientists led by Burckhard Seelig of the University of Minnesota have now determined the unique structure of this novel biocatalyst using NMR and synchrotron-based Zn K-edge EXAFS at SSRL's Beam Line 9-3

  • The Elements of Stroke

    Brain injuries from stroke are both common and costly. The NIH has estimated that the total annual cost of stroke in the United States is $43 billion including direct medical care and the costs related to lost productivity. It has been recognized that rapid diagnosis and treatment is essential to limit neuronal cell death from either a bleed into the brain (hemorrhagic stroke) or a blockage that deprives part of the brain of oxygen (ischemic stroke). The Synchrotron Medical Imaging Team, a group of Canadian, US, and European scientists from diverse backgrounds are collaborating to better understand the underlying chemistry of stroke and how to best image and treat stroke patients.

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