Solvent Accessibility Mapping
Solvent Accessibility Mapping - Related Videos
01:12
Solvents
0 Views •
2019
A solvent is a substance, most often a liquid, that can dissolve other substances. Here, the substance being dissolved is called a solute. When a solvent and a solute combine, they form a solution - a homogenous mixture of both the solvent and the solute. Water is a universal biological solvent. Its polar structure allows it to dissolve many other polar compounds. The ability of water to dissolve is governed by a balance between water molecules binding to each other and binding to the solute. A...
06:43
Rotary Evaporation to Remove Solvent
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2023
Source: Dr. Melanie Pribisko Yen and Grace Tang — California Institute of Technology Rotary evaporation is a technique most commonly used in organic chemistry to remove a solvent from a higher-boiling point compound of interest. The rotary evaporator, or "rotovap", was invented in 1950 by the chemist Lyman C. Craig. The primary use of a rotovap is to dry and purify samples for downstream applications. Its speed and ability to handle large volumes of solvent make rotary evaporation a preferred...
09:41
Schlenk Lines Transfer of Solvents
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2023
Source: Hsin-Chun Chiu and Tyler J. Morin, laboratory of Dr. Ian Tonks—University of Minnesota Twin Cities Schlenk lines and high vacuum lines are both used to exclude moisture and oxygen from reactions by running reactions under a slight overpressure of inert gas (usually N2 or Ar) or under vacuum. Vacuum transfer has been developed as a method separate solvents (other volatile reagents) from drying agents (or other nonvolatile agents) and dispense them to reaction or storage vessels while...
08:14
Analysis of the Solvent Accessibility of Cysteine Residues on Maize rayado fino virus Virus-like Particles Produced in Nicotiana benthamiana Plants and Cross-linking of Peptides to VLPs
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Cited by 3 •
2013
A method to analyze the solvent accessibility of the thiol group of cysteine residues of Maize rayado fino virus (MRFV)-virus-like particles (VLPs) followed by a peptide cross-linking reaction is described. The method takes advantage of the availability of several chemical groups on the surface of the VLPs that can be targets for specific reactions.
08:13
Preparation of Biopolymer Aerogels Using Green Solvents
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Cited by 44 •
2016
A new way for the production of biopolymer-based aerogels by carbon dioxide (CO2) induced gelation is shown. The technique utilizes pressurized carbon dioxide (5 MPa) for the production of biopolymer hydrogels and supercritical CO2 (12 MPa) to convert gels into aerogels. The only solvents needed besides CO2 are water and ethanol.
FAQs
The key signal comes from differential interaction with the surrounding solvent. Solvent-sensitive probes or chemical reagents can reach accessible atoms or residues, whereas buried regions remain protected from those interactions. Mapping where labeling occurs therefore links chemical reactivity to structural exposure, allowing researchers to infer how a biomolecule’s three-dimensional organization positions different regions relative to solvent.
A change in labeling indicates that a region’s exposure has changed under the conditions being compared. This shift can reflect an altered conformation or the formation of a molecular interaction that shields previously accessible atoms or residues, or exposes protected ones. Researchers can therefore use labeling differences to examine structural rearrangements associated with molecular function.
Accessibility patterns provide structural clues about how proteins organize during folding and how their conformations change over time or in response to conditions. Regions that become more exposed or protected can mark structural rearrangements rather than simply showing the protein’s overall shape. These comparisons help connect conformational dynamics with folding behavior and biological function.
When a protein interacts with another molecule, atoms or residues at the contact region may become less accessible to solvent than they were before binding. Comparing labeling patterns in different interaction states can therefore highlight candidate binding interfaces. The resulting structural information helps relate physical contact between molecules to changes in conformation and function.
A basic workflow compares how solvent-sensitive probes or chemical reagents interact with a biomolecule under defined conditions. Researchers then examine the resulting accessibility or labeling patterns and compare them across structural or interaction states. Differences identify regions whose exposure has changed, providing evidence for altered conformation, molecular association, assembly, or environmental response.
Researchers can apply the method when they need structural information about protein folding, binding interfaces, conformational dynamics, or membrane-associated structures. It is especially informative when accessibility patterns can be compared between conditions, because those comparisons reveal how proteins function, assemble, or respond to environmental changes. The approach supports work in molecular biology and biochemistry.
Accessibility maps can support drug development by revealing exposed and protected regions relevant to protein structure and molecular interaction. Patterns that change upon binding or conformational rearrangement may help characterize interaction interfaces and functional states. This structural context can guide investigation of how molecules associate with biological targets, while remaining connected to the protein’s three-dimensional organization.
Condition-to-condition comparisons show whether a biomolecule’s accessible regions remain stable or change during structural and functional transitions. Increased or decreased labeling can indicate altered exposure linked to conformation, interaction, assembly, or environmental response. Interpreting these patterns gives researchers a way to connect molecular changes with protein behavior in biological and biochemical studies.