Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level

2016 ◽  
Vol 116 (9) ◽  
pp. 5432-5463 ◽  
Author(s):  
Otto Dopfer ◽  
Masaaki Fujii
Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6546
Author(s):  
Ruxia Feng ◽  
Yicheng Xu ◽  
Xianglei Kong

Although metal cations are prevalent in biological media, the species of multi-metal cationized biomolecules have received little attention so far. Studying these complexes in isolated state is important, since it provides intrinsic information about the interaction among them on the molecular level. Our investigation here demonstrates the unexpected structural diversity of such species generated by a matrix-assisted laser desorption ionization (MALDI) source in the gas phase. The photodissociation spectroscopic and theoretical study reflects that the co-existing isomers of [Arg+Rb+K−H]+ can have energies ≥95 kJ/mol higher than that of the most stable one. While the result can be rationalized by the great isomerization energy barrier due to the coordination, it strongly reminds us to pay more attention to their structural diversities for multi-metalized fundamental biological molecules, especially for the ones with the ubiquitous alkali metal ions.


Author(s):  
Mary Jane West-Eberhard

Some of the best evidence for combinatorial evolution comes from studies of molecular evolution. This chapter discusses combinatorial molecular evolution and shows that it is facilitated by the same properties of the molecular phenotype—modularity and flexibility—that facilitate combinatorial evolution at higher levels of organization. This is not a review of molecular or genomic evolution, and I am aware that by the time it is published it will lack the latest references even on the few topics discussed. I suspect that continued progress will only make the main point of this chapter more obvious: in many respects, evolution at the molecular level follows the same pattern as that seen at higher levels of organization, for it involves modular reorganization and developmental plasticity as architects of evolutionary change. A combinatorial view of structural change has long been commonplace in chemistry, since all of the materials of the organic and inorganic world come from different combinations of only 112 elements listed in the periodic table. Since biochemistry and molecular biology focus on the fundamentally modular structure and behavior of biological molecules, it is perhaps not surprising that they arrived early at a combinatorial view of evolution, and that it was a molecular biologist (Jacob, 1977) who described evolution as “tinkering” with preexisting pieces. The lowest level of combinatorial evolution is based on the “changeability” of the genetic code— its ability to undergo rearrangement without loss of functionality (Maeshiro and Kimura, 1998). A reorganizational basis for some kinds of mutation was also proposed by premolecular geneticists like H. J. Muller (see discussion of this work in Huxley, 1942, p. 92), who saw minute rearrangements as a kind of mutation distinguishable from “substantive” change of the chromosomal-damage type caused by ultraviolet radiation. More recently, Dickinson (1988) refers to a “combinatorial” model for the evolution of gene regulation. And genetic engineering makes extensive use of combinatorial principles in creating novel substances and genes.


2017 ◽  
Vol 19 (33) ◽  
pp. 22564-22572 ◽  
Author(s):  
Matthias Wohlgemuth ◽  
Mitsuhiko Miyazaki ◽  
Kohei Tsukada ◽  
Martin Weiler ◽  
Otto Dopfer ◽  
...  

Probing solvation dynamics at the molecular level: different water migration pathways around a peptide bond.


2005 ◽  
Vol 19 (04) ◽  
pp. 691-713 ◽  
Author(s):  
XIAOYUN CHEN ◽  
MATTHEW L. CLARKE ◽  
JIE WANG ◽  
ZHAN CHEN

Sum frequency generation (SFG) vibrational spectroscopy has been employed to study a variety of interesting biological phenomena occurring at interfaces. This review summarizes recent SFG studies on proteins, lipid monolayers and bilayers, and other biological molecules. Molecular level details revealed by SFG in these studies show that SFG is a powerful technique for characterizing conformation, orientation and ordering of biological molecules at interfaces.


2021 ◽  
Vol 14 (4) ◽  
pp. 1428-1434
Author(s):  
Krishnendu Adhikary

The sphere of Nanotechnology encompasses most of our lives and houses biomedicine and biomedical advancements. Nanoparticles owing to their minuscule sizes and due to various physicochemical and electrical properties have been exploited in pharmaceutical industries, agriculture, packaging, cosmetic, food industries. Nanomedicine is a laboratory-designed molecular-level pharmaceutical material that has revolutionized diagnostic techniques and therapeutics. Nanoscience and nanotechnology and their wide applications have become spread field worldwide because nanomaterials have novel and unique properties. Nanotechnology involves understanding and manipulating materials normally in the size range of 1 to 100 nm, where they show completely novel physicochemical properties from their bulk counterpart. The capacity to study compounds at the molecular level has aided the hunt for materials with exceptional qualities for medical applications. Nanotechnology in recent days is applied in the designing of nano biosensors. Nanobiosensors are biological molecules immobilized onto the surface of a signal transducer. The application of nano biosensors in the field of disease detection has increased in recent years which has influenced in research of cancer and biosensing. Due to the high surface area of nanoparticles, they are important in the production of nano biosensors with high levels of sensitivity and diminish the response times. However, a comprehensive review regarding the type, mode of function, and their application in various diseases is missing. Nano Deterministic lateral displacement technology that provided exosome splitting based on size differences has resulted in providing the much-needed boost to cancer research. The time taken for cancer screening has been reduced drastically. that This review aims to describe the utilization of nano deterministic lateral displacement technology, nano biosensors, and their applications in certain disease diagnoses.


2019 ◽  
Vol 75 (6) ◽  
pp. 523-527
Author(s):  
Eddy Arnold ◽  
Hao Wu ◽  
John E. Johnson

Michael George Rossmann, who made monumental contributions to science, passed away peacefully in West Lafayette, Indiana on 14 May 2019 at the age of 88, following a courageous five-year battle with cancer. Michael was born in Frankfurt, Germany on 30 July 1930. As a young boy, he emigrated to England with his mother just as World War II ignited. Michael was a highly innovative and energetic person, well known for his intensity, persistence and focus in pursuing his research goals. Michael was a towering figure in crystallography as a highly distinguished faculty member at Purdue University for 55 years. Michael made many seminal contributions to crystallography in a career that spanned the entirety of structural biology, beginning in the 1950s at Cambridge where the first protein structures were determined in the laboratories of Max Perutz (hemoglobin, 1960) and John Kendrew (myoglobin, 1958). Michael's work was central in establishing and defining the field of structural biology, which amazingly has described the structures of a vast array of complex biological molecules and assemblies in atomic detail. Knowledge of three-dimensional biological structure has important biomedical significance including understanding the basis of health and disease at the molecular level, and facilitating the discovery of many drugs.


2020 ◽  
Vol 295 (51) ◽  
pp. 17602-17623
Author(s):  
Justin M. Bradley ◽  
Dimitry A. Svistunenko ◽  
Michael T. Wilson ◽  
Andrew M. Hemmings ◽  
Geoffrey R. Moore ◽  
...  

Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable “free” iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can also lead to the formation of reactive nitrogen species. To avoid iron-mediated oxidative stress, bacteria utilize iron-dependent global regulators to sense the iron status of the cell and regulate the expression of proteins involved in the acquisition, storage, and efflux of iron accordingly. Here, we survey the current understanding of the structure and mechanism of the important members of each of these classes of protein. Diversity in the details of iron homeostasis mechanisms reflect the differing nutritional stresses resulting from the wide variety of ecological niches that bacteria inhabit. However, in this review, we seek to highlight the similarities of iron homeostasis between different bacteria, while acknowledging important variations. In this way, we hope to illustrate how bacteria have evolved common approaches to overcome the dual problems of the insolubility and potential toxicity of iron.


Author(s):  
F.J. Sjostrand

In the 1940's and 1950's electron microscopy conferences were attended with everybody interested in learning about the latest technical developments for one very obvious reason. There was the electron microscope with its outstanding performance but nobody could make very much use of it because we were lacking proper techniques to prepare biological specimens. The development of the thin sectioning technique with its perfectioning in 1952 changed the situation and systematic analysis of the structure of cells could now be pursued. Since then electron microscopists have in general become satisfied with the level of resolution at which cellular structures can be analyzed when applying this technique. There has been little interest in trying to push the limit of resolution closer to that determined by the resolving power of the electron microscope.


Author(s):  
J. Langmore ◽  
M. Isaacson ◽  
J. Wall ◽  
A. V. Crewe

High resolution dark field microscopy is becoming an important tool for the investigation of unstained and specifically stained biological molecules. Of primary consideration to the microscopist is the interpretation of image Intensities and the effects of radiation damage to the specimen. Ignoring inelastic scattering, the image intensity is directly related to the collected elastic scattering cross section, σɳ, which is the product of the total elastic cross section, σ and the eficiency of the microscope system at imaging these electrons, η. The number of potentially bond damaging events resulting from the beam exposure required to reduce the effect of quantum noise in the image to a given level is proportional to 1/η. We wish to compare η in three dark field systems.


Author(s):  
S. Cusack ◽  
J.-C. Jésior

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).


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