Protein engineering by chemical methods: Incorporation of nonnatural amino acids as a tool for studying protein folding, stability, and function

2018 ◽  
Vol 110 (5) ◽  
pp. e24090
Author(s):  
Vincenzo De Filippis ◽  
Nicola Pozzi ◽  
Laura Acquasaliente ◽  
Ilaria Artusi ◽  
Giulia Pontarollo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Engineering ◽  
Chemical Methods ◽  
Nonnatural Amino Acids ◽  
And Function

3. Proteins

2021 ◽  
pp. 34-51
Author(s):  
Mark Lorch
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structure ◽  
Protein Structures ◽  
Structure And Function ◽  
Vast Array ◽  
A Cell ◽  
Cellular Machinery ◽  
And Function ◽  
The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

scholarly journals Inteins in Microbial Genomes: Distribution, Mechanism, and Function

2002 ◽  
Vol 2 ◽  
pp. 25-26
Author(s):  
Maurice W. Southworth ◽  
Francine B. Perler
Keyword(s):  
Amino Acids ◽  
Protein Engineering ◽  
Drug Targets ◽  
Engineering Applications ◽  
Microbial Genomes ◽  
Link Type ◽  
On Line ◽  
Pathogenic Microbes ◽  
And Function ◽  
Self Splicing

Inteins are self-splicing protein elements (134 to 608 amino acids). Over 125 inteins have been cataloged in InBase, the on-line intein database (http://www.neb.com/neb/inteins.html), which includes the Intein Registry[1]. Inteins naturally present in pathogenic microbes represent novel, yet unexploited drug targets. Understanding the chemistry of the splicing reaction has allowed the manipulation of inteins, which are now used in many protein engineering applications[2].

scholarly journals Biosynthetic Glycan Labeling

2021 ◽  
Author(s):  
Victoria M Marando ◽  
Daria E Kim ◽  
Phillip J Calabretta ◽  
Matthew B Kraft ◽  
Bryan D Bryson ◽  
...  
Keyword(s):  
Amino Acids ◽  
Cell Wall ◽  
Genetic Manipulation ◽  
Building Blocks ◽  
Structure And Function ◽  
Covalent Modification ◽  
Asymmetric Distribution ◽  
Chemical Methods ◽  
And Function ◽  
Glycan Modification

Glycans are ubiquitous and play important biological roles, yet chemical methods for probing their structure and function within cells remain limited. Strategies for studying other biomacromolecules, such as proteins, often exploit chemoselective reactions for covalent modification, capture, or imaging. Unlike amino acids that constitute proteins, glycan building blocks lack distinguishing reactivity because they are composed primarily of polyol isomers. Moreo-ver, encoding glycan variants through genetic manipulation is complex. Therefore, we formulated a new, generaliza-ble strategy for chemoselective glycan modification that directly takes advantage of cellular glycosyltransferases. Many of these enzymes are selective for the products they generate yet promiscuous in their donor preferences. Thus, we designed reagents with bioorthogonal handles that function as glycosyltransferase substrate surrogates. We validated the feasibility of this approach by synthesizing and testing probes of D-arabinofuranose (D-Araf), a monosaccharide found in bacteria and an essential component of the cell wall that protects mycobacteria, including Mycobacterium tuberculosis. The result is the first probe capable of selectively labeling arabinofuranose-containing glycans. Our stud-ies serve as a platform for developing new chemoselective labeling agents for other privileged monosaccharides. This probe revealed an asymmetric distribution of D-Araf residues during mycobacterial cell growth and could be used to detect mycobacteria in THP1-derived macrophages.

Research Regarding Content in Amino-acids and Biological Value of Proteins from Polyodon spathula Sturgeon Meat

2017 ◽  
Vol 68 (5) ◽  
pp. 1063-1069
Author(s):  
Cristina Simeanu ◽  
Daniel Simeanu ◽  
Anca Popa ◽  
Alexandru Usturoi ◽  
Dan Bodescu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nutritive Value ◽  
Essential Amino Acids ◽  
Meat Production ◽  
Age Group ◽  
Chemical Methods ◽  
Biological Value ◽  
Polyodon Spathula ◽  
The One ◽  
Total Amino Acids

Polyodon spathula sturgeon breed is successfully reared in Romania in many fishery farms for meat production and it is capitalized on domestic market as consumption fish. In the current paper were studied a number of 1400 sturgeons from Polyodon spathula breed (1200 individuals of one summer - P.s.0+ and 200 individuals of fourth summers - P.s.3+). From this flock were weighted around 10%, for each age group, and for laboratory determinations were chosen 10 fishes for each age with the corporal mass close to the group mean. After analysing the fillets gathered from the studied fishes for establishing the chemical characteristics, nutritive and biological values of proteins were drawn some interesting conclusions. So, regarding chemical composition we notice that in the meat of analysed fishes water is in a rate of 75.41% at P.s.3+ and 78.37% for P.s.0+; proteins - between 18.08% for P.s.0+ and 19.89% for P.s.3+, values which place those fishes in the group of protein fishes; lipids - between 2.45% and 3.45%, values which situated those sturgeons in category of fishes with a low content in lipids; collagen � 3.83% at P.s.0+ and 4.14% at P.s.3+ which indicate low values for proteins of weak quality in the meat of those sturgeons. Study of nutritive value for the analysed fishes indicate the fact that fishes P.s.0+ have a mediocre nutritive value, having the ratio w/p of 4.33 while sturgeons P.s.3+ were placed in the 2nd category � fishes with a good nutritive value (rate w/p = 3.79). Energetic value of the studied fillets was 97.39 kcal/100 g for P.s.0+ and 114.31 kcal/100 g for P.s.3+, which enlightened an increase of nutritive value with aging, fact especially due to accumulation of adipose tissue. Study of proteins quality, through the presence of those 8 essential amino-acids in the meat of analysed fishes, show the fact that at sturgeons P.s.0+ proportion of essential amino-acids was 20.88% from total amino-acids, while at sturgeons P.s.3+ was 26.23%, fact which enlightened an increasing of proteins� biological value with fish aging. This fact was also shown by calculation of proteins� biological value through chemical methods (EAA index); calculated value for sturgeons P.s.0+ was a little bit lower (118.73) than the one calculated for sturgeons P.s.3+ (118.79).

Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana

2021 ◽  
Author(s):  
Shen Jean Lim ◽  
Brenton Davis ◽  
Danielle Gill ◽  
John Swetenburg ◽  
Laurie C Anderson ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nutrient Cycling ◽  
Bacterial Communities ◽  
Structure And Function ◽  
Differentially Expressed ◽  
Seagrass Species ◽  
Bare Sand ◽  
And Function

Abstract Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic, and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides, and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes, and their environment.

scholarly journals Time-dependent communication between multiple amino acids during protein folding

2021 ◽  
Vol 12 (16) ◽  
pp. 5944-5951
Author(s):  
Song-Ho Chong ◽  
Sihyun Ham
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Transition State ◽  
Time Dependent ◽  
Transition Path ◽  
Contact Formation ◽  
Molecular Origin

Cooperativity in contact formation among multiple amino acids starts to develop upon entering the folding transition path and attains a maximum at the folding transition state, providing the molecular origin of the two-state folding behavior.

scholarly journals Cellular and metabolic mechanisms of nutrient actions in immune function

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Philip Newsholme
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Vitamin D ◽  
Immune System ◽  
Cell Function ◽  
Immune Cell ◽  
Cell Structure ◽  
Nutritional Intervention ◽  
Immune Cell Function ◽  
And Function

AbstractVarious nutrients can change cell structure, cellular metabolism, and cell function which is particularly important for cells of the immune system as nutrient availability is associated with the activation and function of diverse immune subsets. The most important nutrients for immune cell function and fate appear to be glucose, amino acids, fatty acids, and vitamin D. This perspective will describe recently published information describing the mechanism of action of prominent nutritional intervention agents where evidence exists as to their action and potency.

scholarly journals Influence of spatial structure on protein damage susceptibility: a bioinformatics approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maximilian Fichtner ◽  
Stefan Schuster ◽  
Heiko Stark
Keyword(s):  
Amino Acids ◽  
Molecular Medicine ◽  
Protein Damage ◽  
Aging Research ◽  
Form And Function ◽  
The Core ◽  
And Function ◽  
Thermophilic Organisms ◽  
Damage Susceptibility ◽  
Protein Shell

AbstractAging research is a very popular field of research in which the deterioration or decline of various physiological features is studied. Here we consider the molecular level, which can also have effects on the macroscopic level. The proteinogenic amino acids differ in their susceptibilities to non-enzymatic modification. Some of these modifications can lead to protein damage and thus can affect the form and function of proteins. For this, it is important to know the distribution of amino acids between the protein shell/surface and the core. This was investigated in this study for all known structures of peptides and proteins available in the PDB. As a result, it is shown that the shell contains less susceptible amino acids than the core with the exception of thermophilic organisms. Furthermore, proteins could be classified according to their susceptibility. This can then be used in applications such as phylogeny, aging research, molecular medicine, and synthetic biology.

Folding of peptides and proteins: role of disulfide bonds, recent developments

2013 ◽  
Vol 4 (6) ◽  
pp. 597-604 ◽  
Author(s):  
Yuji Hidaka ◽  
Shigeru Shimamoto
Keyword(s):  
Protein Folding ◽  
Disulfide Bonds ◽  
Bond Formation ◽  
Difficult Problem ◽  
Chemical Methods ◽  
Mutant Proteins ◽  
Folding Intermediates ◽  
Peptide Chemistry ◽  
Recent Developments

AbstractDisulfide-containing proteins are ideal models for studies of protein folding as the folding intermediates can be observed, trapped, and separated by HPLC during the folding reaction. However, regulating or analyzing the structures of folding intermediates of peptides and proteins continues to be a difficult problem. Recently, the development of several techniques in peptide chemistry and biotechnology has resulted in the availability of some powerful tools for studying protein folding in the context of the structural analysis of native, mutant proteins, and folding intermediates. In this review, recent developments in the field of disulfide-coupled peptide and protein folding are discussed, from the viewpoint of chemical and biotechnological methods, such as analytical methods for the detection of disulfide pairings, chemical methods for disulfide bond formation between the defined Cys residues, and applications of diselenide bonds for the regulation of disulfide-coupled peptide and protein folding.

Robustness and generalization of structure-based models for protein folding and function

2009 ◽  
Vol 77 (4) ◽  
pp. 881-891 ◽  
Author(s):  
Heiko Lammert ◽  
Alexander Schug ◽  
José N. Onuchic
Keyword(s):  
Protein Folding ◽  
And Function
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