Catalysis

Structural Evidence that Rodents Facilitated the Evolution of the SARS-CoV-2 Omicron Variant

December 19, 2022

The omicron variant of COVID-19 was identified in the fall of 2021. It stood out from all of the other variants because of the many mutations that simultaneously occurred in its spike protein1. So far, surveillance and bioinformatics have been the main scientific tools in tracking COVID-19 evolution. Eventually, however, understanding COVID-19 evolution comes down to understanding the functions of key viral mutations. This is where structural biology kicks in and plays a critical role in tracking COVID-19 evolution.

Direct Observation of the Kinetics of Gas–Solid Reactions Using in-Situ Kinetic and Spectroscopic Techniques

August 31, 2018

Hydrogen sulfide (H2S) is a poisonous and corrosive gas created in industrial and natural systems. Copper oxide (CuO), a crystalline solid, can be used to clean H2S from emissions by forming various copper sulfide species, a reaction that is thermodynamically favorable but often does not go to completion in industrial applications.

An Oxygen-insensitive Hydrogen Evolution Catalyst Coated by a Molybdenum-based Layer for Overall Water Splitting

July 31, 2017

Molecular hydrogen (H2) is a promising carrier of energy for a future that uses more sustainable sources of fuel. H2 created from splitting H2O using renewable energy methods could result in no carbon footprint energy use. While methods of water splitting are being developed, reverse reactions are a problem.

Insights into the Role of the Tyr-Cys Cross-link in Galactose Oxidase from Sulfur K-edge Spectroscopy

May 29, 2012

The continuous advancement of X-ray spectroscopic techniques allows us to probe the structure of biological machineries for smaller samples in more dilute concentrations and thus to ask tough scientific questions about problems that have not been possible in the past. Careful biochemical preparation and systematic analytical characterization resulted in galactose oxidase samples that could be interrogated by X-rays. This metalloenzyme contains a copper at its active site that is coordinated to a cross-linked tyrosine and cysteine ligand, which both are essential to convert alcohols and sugars to their oxidized aldehyde forms by oxygen molecule. The remarkable feature of this reaction that it is selective and does not results in formation of carboxylates (a form of vinegar).

Structure of a Cation-bound Multidrug and Toxic Compound Extrusion Transporter

October 25, 2010

MATE transporters are responsible for the exportation of various substrates and toxins from cells of bacteria, plants, and mammals using a proton or sodium gradient. Plants use them to transport metabolites, and they are important for tolerance to aluminum in soil, an important factor for crop yield. In bacteria and mammals, MATE transporters are important for multiple-drug resistance, which affects the efficacy of many medicines. Although these transporters play such important roles, much about how they work is not understood.

Spotting Disease Hot Spots in Ryanodine Receptors

November 29, 2010

Our bodies heavily rely on calcium ions (Ca2+). Their concentration in the cell cytoplasm is normally low under resting conditions, and its influx through specialized ion channels drives many functions ranging from muscle contraction, regulating heart beats, secretion of hormones and neurotransmitter, transcription of specific genes, and more. Ca2+ can enter the cytoplasm either from the extracellular space, or from intracellular stores.

A Bacterium that can Grow by Using Arsenic Instead of Phosphorus

December 14, 2010

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorous.  Although these six elements make up biomolecules such as nucleic acids, proteins, and lipids, it is theoretically possible that some other elements in the periodic table could serve similar functions.  In a paper published in Science, Wolfe-Simon et. al., describe a bacterium of the Halomonadaceae family, strain GFAJ-1 which appears to substitute arsenic for phosphorous to sustain its growth.

Synchrotron X-ray Analysis Demonstrate Phosphate-Bound Gadolinium in Skin in Nephrogenic Systemic Fibrosis

December 13, 2010

Nephrogenic systemic fibrosis, or NSF, is a relatively new disease in which the skin becomes hardened, joint movement becomes difficult and, in extreme cases, an excessive and sometimes fatal fibrosis tissue forms around organs. So far, NSF has only been observed in patients with kidney dysfunction who have undergone an MRI that required the injection of gadolinium-based contrast agents (GBCAs). Researchers speculate that the patient's kidneys cannot break down the gadolinium, causing NSF, but until now there has been no direct evidence for such a link.

Electrochemical Surface Science: Hard X-rays Probe Fuel Cell Model Catalyst in situ

December 14, 2010

Researchers at SSRL have developed a new, more powerful way to probe the behavior of a key component in hydrogen fuel cells. The group, led by Daniel Friebel of SSRL and Anders Nilsson of SSRL and SIMES, coated a single crystal of rhodium with one layer of platinum atoms, creating a platinum catalyst that was in essence "all surface." The unique sample design allowed them to observe how the catalyst surface interacted with the type of acid–water environment typical of fuel cells.

Metal templated protein interface design

January 31, 2011

It took nature billions of years to evolve proteins that can selectively bind to certain metals. Researchers are now seeking to create such proteins synthetically in the lab, with the end-goal of creating new metal-based functions.

Electronic Structure of O2-Bound Metal Sites in Biomimetic Model Complexes

March 28, 2011

Dioxygen (O2), critical for many of our cellular processes, is carried and activated by a variety of enzymes. These enzymes contain metals that contact the oxygen in different ways to form reactive intermediates. Oxygen’s reactivity is affected by the arrangement of the enzymes’ amino acid residues. Often, the enzyme active site will have a unique structure to stabilize oxygen binding.

Techniques for Identifying and Mapping Iron Species in Geologic Samples

August 29, 2011

Iron, one of the most abundant metals on Earth’s surface, often dominates the reactivity of rocks, soils and sediments, and is important in many biogeochemical processes.  A great challenge for biogeochemists is to identify the iron species in these natural materials at very small scales and to track changes in the iron species as these materials react with water.

Structure and Reactivity of a Mononuclear Non-Haem Iron(III)–Peroxo Complex

November 28, 2011

The life-sustaining element oxygen can’t do its job alone. Specialized enzymes, containing metallic elements including iron, cause O2to split into two separate oxygen atoms.  In this form, oxygen can react with other biological molecules. The precise mechanism of oxygen activation by iron complexes has long eluded researchers, in part because the reaction—which proceeds through multiple intermediate stages—happens in mere fractions of a second.

Manganese-II Oxidation: A Biotic and Abiotic Process

December 12, 2011

Manganese, one of the most abundant metals in soils and rocks, is important to the health of the environment: As it cycles between manganese-II and nanocrystalline manganese-III/IV oxides, it plays an important role in controlling the cycle and transport of soil nutrients and contaminants.  Yet because the process is kinetically hindered, manganese will not oxidize rapidly in air; manganese needs a catalyst, often bacteria, to spur the process into action.

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