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.

Small membrane proteins – elucidating the function of the needle in the haystack

2014 ◽  
Vol 395 (12) ◽  
pp. 1365-1377 ◽  
Author(s):  
Grant Kemp ◽  
Florian Cymer
Keyword(s):  
Amino Acids ◽  
Membrane Proteins ◽  
Soluble Proteins ◽  
Structure And Function ◽  
Ribosome Profiling ◽  
Water Soluble ◽  
Eukaryotic Cells ◽  
Large Numbers ◽  
A Cell ◽  
And Function

Abstract Membrane proteins are important mediators between the cell and its environment or between different compartments within a cell. However, much less is known about the structure and function of membrane proteins compared to water-soluble proteins. Moreover, until recently a subset of membrane proteins, those shorter than 100 amino acids, have almost completely evaded detection as a result of technical difficulties. These small membrane proteins (SMPs) have been underrepresented in most genomic and proteomic screens of both pro- and eukaryotic cells and, hence, we know much less about their functions in both. Currently, through a combination of bioinformatics, ribosome profiling, and more sensitive proteomics, large numbers of SMPs are being identified and characterized. Herein we describe recent advances in identifying SMPs from genomic and proteomic datasets and describe examples where SMPs have been successfully characterized biochemically. Finally we give an overview of identified functions of SMPs and speculate on the possible roles SMPs play in the cell.

The T3 Method (“T3 It!”): Transcribe → Translate → Transform

2017 ◽  
Vol 79 (4) ◽  
pp. 257-271
Author(s):  
Brett Malas
Keyword(s):  
Protein Folding ◽  
Protein Structure ◽  
Differentiated Instruction ◽  
Genetic Information ◽  
Structural Models ◽  
Structure And Function ◽  
Protein Structure And Function ◽  
Learning Contexts ◽  
Wide Range ◽  
And Function

Traditional transcription-translation exercises are instructionally incomplete by failing to link prescriptive genetic information with protein structure and function. The T3 Method solves this problem by adding a conceptually powerful yet easily learned third step where students use simple protein folding codes to transform their translations into corresponding protein structural models. This brings structural sense to sequence and makes the information-to-proteins connection that is so profoundly important to understand in biology more directly evident, experiential, and intrinsically meaningful. The T3 Method has further utility, proving versatile and adaptive to a wide range of academic levels and learning contexts, with possibilities for differentiated instruction, application, and extension.

PlaneFinder: a methodology to find the best plane for a set of atoms involved in the metal coordination in protein structures

2018 ◽  
Vol 51 (4) ◽  
pp. 1251-1256
Author(s):  
J. Janu Sahana ◽  
S. Sriraghav ◽  
T. A. Vijeth ◽  
T. Nagarushyanth ◽  
R. Santhosh ◽  
...  
Keyword(s):  
Protein Structure ◽  
Efficient Method ◽  
Protein Structures ◽  
Three Dimensional ◽  
Structure And Function ◽  
The Other ◽  
Metal Coordination ◽  
And Function ◽  
Interacting Atoms ◽  
Best Fit

Metal ions play a considerable role in protein structure and function. The roles of most metals and their importance are determined by the arrangements of the interacting atoms in the three-dimensional protein structure. This information is essential in predicting the geometry of the atoms involved in metal coordination. The deviation of the other atoms from the best plane is another crucial factor. The proposed web server, PlaneFinder, provides a fast and efficient method to calculate the best-fit plane for a set of atoms involved in the metal coordination. It provides in addition other possible planes by considering the maximum number of interacting atoms as well as user-selected atoms. The deviations of the selected atoms and other atoms from the best-fit plane are also displayed. PlaneFinder is freely available and can be accessed at http://bioserver1.physics.iisc.ac.in/plane/.

scholarly journals The Structure ofampGGene inPseudomonas aeruginosaand Its Effect on Drug Resistance

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Qingli Chang ◽  
Chongyang Wu ◽  
Chaoqing Lin ◽  
Peizhen Li ◽  
Kaibo Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Inhibitory Concentration ◽  
Normal Function ◽  
Structure And Function ◽  
Clinical Isolates ◽  
Site Specific ◽  
Directed Mutation ◽  
And Function ◽  
The Relationship

In order to study the relationship between the structure and function of AmpG, structure, site-specific mutation, and gene complementary experiments have been performed against the clinical isolates ofPseudomonas aeruginosa. We found that there are 51 nucleotide variations at 34 loci over theampGgenes from 24 of 35P. aeruginosastrains detected, of which 7 nucleotide variations resulted in amino acid change. TheampGvariants with the changed nucleotides (amino acids) could complement the function ofampGdeleted PA01 (PA01ΔG). The ampicillin minimum inhibitory concentration (MIC) of PA01ΔG complemented with 32ampGvariants was up to 512 μg/ml, similar to the original PA01 (P. aeruginosa PA01). Furthermore, site-directed mutation of two conservative amino acids (I53 and W90) showed that when I53 was mutated to 53S or 53T (I53S or I53T), the ampicillin MIC level dropped drastically, and the activity of AmpCβ-lactamase decreased as well. By contrast, the ampicillin MIC and the activity of AmpCβ-lactamase remained unchanged for W90R and W90S mutants. Our studies demonstrated that although nucleotide variations occurred in most of theampGgenes, the structure of AmpG protein in clinical isolates is stable, and conservative amino acid is necessary to maintain normal function of AmpG.

scholarly journals Identification of Yak’s TLR4 Alternative Spliceosomes and Bioinformatic Analysis of TLR4 Protein Structure and Function

Animals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 32
Author(s):  
Xingdong Wang ◽  
Jie Pei ◽  
Pengjia Bao ◽  
Chunnian Liang ◽  
Min Chu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Disease Resistance ◽  
Protein Structure ◽  
Bioinformatic Analysis ◽  
Structure And Function ◽  
Sequence Length ◽  
Exon 2 ◽  
Expression Levels ◽  
Tlr4 Gene ◽  
And Function

In this study, the yak’s TLR4 gene alternative spliceosomes were investigated using PCR amplification and cloning to improve disease-resistance in yak and promote efficient utilization of yak’s resources. qRT-PCR was used to determine the expression levels of two alternatively spliced transcripts of the TLR4 gene in seven distinct tissues. To predict the function of proteins expressed by each TLR4 spliceosome, bioinformatic analysis of yak’s TLR4 protein structure and function was performed, which led to the identification of two alternative spliceosomes of yak’s TLR4 gene. The TLR4-X1 sequence length was 2526 bp, and it encoded full-length TLR4 protein (841 amino acids). The sequence length of the exon-2 deleted TLR4-X2 sequence was 1926 bp, and it encoded truncated TLR4 protein (641 amino acids). TLR4-X2 sequence was consistent with the predicted sequence of the TLR4 gene in GenBank. Each tissue showed significantly different expression levels of these two alternative spliceosomes. As per the bioinformatic analysis of the structure and function of TLR4 protein, deletion of exon-2 in the TLR4 gene resulted in frameshift mutations of the reading frame in the corresponding protein, which altered its ligand-binding and active sites. Besides, biological property such as substrate specificity of truncated TLR4 protein was also altered, leading to altered protein function. This study has laid a theoretical foundation for exploring the role of two variants of the TLR4 gene in yak’s disease resistance. Besides, this study’s data could be analyzed further to explore the molecular mechanism associated with disease-resistance in the yak.

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