New technique could provide insights about behavior of biomolecules in watery environments

Scientists have measured for the first time at the nanometer scale the characteristic patterns of folds responsible for proteins to know their three-dimensional shape in water with the help of the method developed earlier. With the help of this technique, scientists will be able to gain insights about the behavior of biomolecules in watery environments. These insights will result into increase in understanding the major diseases including Alzheimer's, that are related to "mistakes" in protein folding.

We would not be able survive life if proteins didn't fold into precise patterns resulting into helices, sheets and other shapes that give proteins their three-dimensional structure. The precise shapes of p Scientists have measured for the first time at the nanometer scale the characteristic patterns of folds responsible for proteins to know their three-dimensional shape in water with the help of the method developed earlier. With the help of this technique, scientists will be able to gain insights about the behavior of biomolecules in watery environments. These insights will result into increase in understanding the major diseases including Alzheimer's, that are related to "mistakes" in protein folding. Proteins are responsible to carry oxygen, fend off harmful bacteria and perform other essential tasks in the body. When proteins fail to fold improperly and cannot function regularly and then sometimes they generate toxic fragments such as those associated with neurodegenerative disorders.

To understand the complexity of folding, scientists requires to study the detailed arrangement of amino acids in a chain which are shorter and simpler than proteins referred to as peptides, the mechanism of their folding, assembling and rotation to create a different shapes or conformations. Biologists usually prefer to examine proteins and peptides immersed in water because the environment closely relates to the conditions inside a living cell.

Earlier discovered techniques for determining the conformation of proteins including infrared spectroscopy are lacking the spatial resolution which is necessary to study the tiny and diverse assemblies of properly folded and misfolded. The drawback with these techniques is that they are not working well in an aqueous environment due to water’s tendency to absorbs infrared light. Water posed several challenges to photo-thermal induced resonance (PTIR) enabling the researchers to examine peptide structure for conformation in air at nanoscale resolution.

Researchers also demonstrated, if PTIR can be adapted to obtain conformational structure at the nanoscale in water by using two chemically similar peptides. PTIR is among the powerful techniques showing promise to study the biological systems, but the possibility to use this with samples in a liquid environment will greatly improve its use in this area. PTIR is used to determines the chemical composition of materials by combining an atomic force microscope (AFM) along with the light from an infrared laser operating over a range of wavelengths. The characteristic wavelengths of infrared light that are absorbed by the sample are alike a molecular fingerprint which tells about its chemical composition. The material heats up at every site where the infrared is absorbed causing it to rapidly to expand. The expansion is detected with the help a sharp tip of the AFM which protrudes from a cantilever oscillating like a diving board when each time the sample expands. More light that is absorbed by the sample with the greater expansion and larger is the strength or amplitude of the oscillations.

PTIR also have some disadvantage associated with it in water environment. Water strongly absorbs infrared light, producing an absorption signal that can interfere with efforts to discern the sample's chemical structure. The drag force is also exerted by water which is much stronger than in air, weakening the PTIR signal due to strongly damping of the oscillations of the AFM's cantilever.

To limit the water's absorption for infrared light, a prism between the laser and the sample. The prism serves to confine the infrared light to the sample's surface by thus minimizing the amount that could leak out and interact with the water. To address the damping problem, a laser is used that could operate at frequencies up to 2,000 kHz. This enables the researchers to match the frequency of the laser pulses to one of the higher frequencies of the cantilever oscillates.

The efficiency of the method was confirmed by the researchers by comparing PTIR measurements of diphenylalanine and other peptide samples under two conditions, water, and air respectively. The peptides folded similarly in both mediums, which made the comparison easier. Scientists have achieved similar spatial resolution for both water and air, enabling them to demonstrate the measurements in a water environment which can be performed accurately thus depicting the precise conformation of peptides with nanoscale resolution.

Therefore, this finding is important to biologists who want to understand protein structure and folding in environments as close as possible to those in living cells.