scholarly journals Estimating the Designability of Protein Structures

2021 ◽  
Author(s):  
Feng Pan ◽  
Yuan Zhang ◽  
Xiuwen Liu ◽  
Jinfeng Zhang
Keyword(s):  
Deep Neural Network ◽  
Sequential Monte Carlo ◽  
Protein Structures ◽  
Fundamental Property ◽  
Lattice Models ◽  
Structure And Function ◽  
Amino Acid Sequences ◽  
Sequential Monte Carlo Method ◽  
Backbone Structure ◽  
And Function

The total number of amino acid sequences that can fold to a target protein structure, known as "designability", is a fundamental property of proteins that contributes to their structure and function robustness. The highly designable structures always have higher thermodynamic stability, mutational stability, fast folding, regular secondary structures, and tertiary symmetries. Although it has been studied on lattice models for very short chains by exhaustive enumeration, it remains a challenge to estimate the designable quantitatively for real proteins. In this study, we designed a new deep neural network model that samples protein sequences given a backbone structure using sequential Monte Carlo method. The sampled sequences with proper weights were used to estimate the designability of several real proteins. The designed sequences were also tested using the latest AlphaFold2 and RoseTTAFold to confirm their foldabilities. We report this as the first study to estimate the designability of real proteins.

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 Primary structure of OXA-3 and phylogeny of oxacillin-hydrolyzing class D beta-lactamases.

1995 ◽  
Vol 39 (4) ◽  
pp. 887-893 ◽  
Author(s):  
F Sanschagrin ◽  
F Couture ◽  
R C Levesque
Keyword(s):  
Amino Acids ◽  
Structure And Function ◽  
Amino Acid Sequences ◽  
Specific Class ◽  
Conserved Motifs ◽  
Beta Lactamases ◽  
Class A ◽  
Class D ◽  
And Function ◽  
Conserved Amino Acids

We determined the nucleotide sequence of the blaOXA-3(pMG25) gene from Pseudomonas aeruginosa. The bla structural gene encoded a protein of 275 amino acids representing one monomer of 31,879 Da for the OXA-3 enzyme. Comparisons between the OXA-3 nucleotide and amino acid sequences and those of class A, B, C, and D beta-lactamases were performed. An alignment of the eight known class D beta-lactamases including OXA-3 demonstrated the presence of conserved amino acids. In addition, conserved motifs composed of identical amino acids typical of penicillin-recognizing proteins and specific class D motifs were identified. These conserved motifs were considered for possible roles in the structure and function of oxacillinases. On the basis of the alignment and identity scores, a dendrogram was constructed. The phylogenetic data obtained revealed five groups of class D beta-lactamases with large evolutionary distances between each group.

scholarly journals Insulin-like growth factors 1 and 2 in bovine colostrum. Sequences and biological activities compared with those of a potent truncated form

1988 ◽  
Vol 251 (1) ◽  
pp. 95-103 ◽  
Author(s):  
G L Francis ◽  
F M Upton ◽  
F J Ballard ◽  
K A McNeil ◽  
J C Wallace
Keyword(s):  
Growth Factors ◽  
Biological Activities ◽  
Structure And Function ◽  
Bovine Colostrum ◽  
Amino Acid Sequences ◽  
Truncated Form ◽  
Reverse Phase ◽  
And Function ◽  
Stimulation Of ◽  
Insulin Like Growth Factors

1. Insulin-like growth factors 1 and 2 (IGF-1 and IGF-2) together with a truncated form of IGF-1 were purified to homogeneity from bovine colostrum. 2. Two forms of IGF-1 were totally resolved from IGF-2 in the purification by h.p.l.c. involving cation-exchange and reverse-phase columns. 3. The complete amino acid sequences for all three forms of IGF were determined. The sequence of bovine IGF-1 was found to be identical with that of human IGF-1, and that of the variant lacked the N-terminal tripeptide Gly-Pro-Glu (-3N:IGF-1). Bovine IGF-2 was found to differ in three residues of the C-domain compared with human IGF-2, with serine, isoleucine and asparagine substituted for alanine, valine and serine respectively at positions 32, 35 and 36. 4. Protein synthesis in L6 rat myoblasts was stimulated and protein degradation inhibited in a co-ordinate response with all three IGFs. The relative potency in both processes was −3N:IGF-1 greater than IGF-1 greater than IGF-2. A similar order of potency was obtained for the stimulation of DNA synthesis by −3N:IGF-1 and IGF-1. The approximately 10-fold effect on biological activity of removing the N-terminal tripeptide is unexpected in view of current information on IGF-1 structure and function.

scholarly journals Better together: building protein oligomers naturally and by design

2019 ◽  
Vol 47 (6) ◽  
pp. 1773-1780 ◽  
Author(s):  
Rebecca E.A. Gwyther ◽  
D. Dafydd Jones ◽  
Harley L. Worthy
Keyword(s):  
Function Space ◽  
Structural State ◽  
Protein Structures ◽  
Structure And Function ◽  
New Approach ◽  
Biological Perspective ◽  
Sample Structure ◽  
Single Polypeptide ◽  
Monomeric Proteins ◽  
And Function

Protein oligomers are more common in nature than monomers, with dimers being the most prevalent final structural state observed in known structures. From a biological perspective, this makes sense as it conserves vital molecular resources that may be wasted simply by generating larger single polypeptide units, and allows new features such as cooperativity to emerge. Taking inspiration from nature, protein designers and engineers are now building artificial oligomeric complexes using a variety of approaches to generate new and useful supramolecular protein structures. Oligomerisation is thus offering a new approach to sample structure and function space not accessible through simply tinkering with monomeric proteins.

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 Uroplakins Ia and Ib, two major differentiation products of bladder epithelium, belong to a family of four transmembrane domain (4TM) proteins.

1994 ◽  
Vol 125 (1) ◽  
pp. 171-182 ◽  
Author(s):  
J Yu ◽  
J H Lin ◽  
X R Wu ◽  
T T Sun
Keyword(s):  
Transmembrane Domain ◽  
Structure And Function ◽  
Amino Acid Sequences ◽  
Transmembrane Domains ◽  
Lung Epithelial Cells ◽  
Apical Surface ◽  
Bladder Epithelium ◽  
Differentiation Markers ◽  
Protein Particles ◽  
And Function

The mammalian bladder epithelium elaborates, as a terminal differentiation product, a specialized plasma membrane called asymmetric unit membrane (AUM) which is believed to play a role in strengthening and stabilizing the urothelial apical surface through its interactions with an underlying cytoskeleton. Previous studies indicate that the outer leaflet of AUM is composed of crystalline patches of 12-nm protein particles, and that bovine AUMs contain three major proteins: the 27- to 28-kD uroplakin I, the 15-kD uroplakin II and the 47-kD uroplakin III. As a step towards elucidating the AUM structure and function, we have cloned the cDNAs of bovine uroplakin I (UPI). Our results established the existence of two isoforms of bovine uroplakin I: a 27-kD uroplakin Ia and a 28-kD uroplakin Ib. These two glycoproteins are closely related with 39% identity in their amino acid sequences. Hydropathy plot revealed that both have four potential transmembrane domains (TMDs) with connecting loops of similar length. Proteolytic digestion of UPIa inserted in vitro into microsomal vesicles suggested that its two main hydrophilic loops are exposed to the luminal space, possibly involved in interacting with the luminal domains of other uroplakins to form the 12-nm protein particles. The larger loop connecting TMD3 and TMD4 of both UPIa and UPIb contains six highly conserved cysteine residues; at least one centrally located cysteine doublet in UPIa is involved in forming intramolecular disulfide bridges. The sequences of UPIa and UPIb (the latter is almost identical to a hypothetical, TGF beta-inducible, TI-1 protein of mink lung epithelial cells) are homologous to members of a recently described family all possessing four transmembrane domains (the "4TM family"); members of this family include many important leukocyte differentiation markers such as CD9, CD37, CD53, and CD63. The tissue-specific and differentiation-dependent expression as well as the naturally occurring crystalline state of uroplakin I molecules make them uniquely suitable, as prototype members of the 4TM family, for studying the structure and function of these integral membrane proteins.

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