Controlled chemical assembly of enzyme in cell lysate enabled by genetic-encoded nonstandard Amino Acid

2021 ◽  
Author(s):  
Jing Zhang ◽  
Ru Wang ◽  
Zhiyuan Luo ◽  
Dongmei Jia ◽  
Haoming Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Biological Materials ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Cell Lysate ◽  
Ordered Nanostructures

Enzyme proteins are nanometer-sized molecules with a three-dimensional structure that can be manipulated and assembled into highly ordered nanostructures, which allows access to advanced biological materials. Here, genetically-encoded nonstandard amino...

PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

1987 ◽  
Author(s):  
A Heckel ◽  
K M Hasselbach
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Three Dimensional Structure ◽  
Insertions And Deletions

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

scholarly journals Amino acid sequence and three-dimensional structure of the Tn-specific isolectin B4 fromVicia villosa

FEBS Letters ◽  
1997 ◽  
Vol 412 (1) ◽  
pp. 190-196 ◽  
Author(s):  
Eduardo Osinaga ◽  
Diana Tello ◽  
Carlos Batthyany ◽  
Mario Bianchet ◽  
Gisele Tavares ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Isolectin B4

scholarly journals Isocitrate dehydrogenase from bovine heart: primary structure of subunit 3/4

1995 ◽  
Vol 310 (2) ◽  
pp. 507-516 ◽  
Author(s):  
Y Zeng ◽  
C Weiss ◽  
T T Yao ◽  
J Huang ◽  
L Siconolfi-Baez ◽  
...  
Keyword(s):  
Amino Acid ◽  
Isocitrate Dehydrogenase ◽  
Three Dimensional ◽  
Alpha Subunit ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Three Dimensional Structure ◽  
Catalytic Function ◽  
N Terminus ◽  
Enzyme Subunits

Bovine NAD(+)-dependent isocitrate dehydrogenase was shown previously to contain four subunits of approx. 40 kDa (subunits 1-4) possessing different peptide maps and electrophoretic properties [Rushbrook and Harvey (1978) Biochemistry 17, 5339-5346]. In this study the heterogeneity is confirmed using enzyme purified by updated methods and from single animals, ruling out allelic variability. Subunits 1 and 2 were differentiated from each other and from subunits 3 and 4 by N-terminal amino acid sequencing. Subunits 3 and 4 (subunits 3/4) were identical in sequence over 30 residues. The N-terminal residues of subunits 1 and 2 were homologous but not identical with the beta- and gamma-subunits respectively of the comparable pig heart enzyme. Subunits 3/4 were identical over 30 residues with the N-terminus of the pig heart alpha-subunit. Full-length sequence, including that for mitochondrial import, is presented for a protein with the processed N-terminus of subunits 3/4, deduced from cloned cDNA obtained utilizing the N-terminal sequence information. The derived amino acid sequence for the mature protein contains 339 amino acids and has a molecular mass of 36,685 Da. Complete identity with N-terminal and Cys-containing peptides totalling 92 residues from the alpha-subunit of the pig heart enzyme [Huang and Colman (1990) Biochemistry 29, 8266-8273] suggests that maintenance of a particular three-dimensional structure in this subunit is crucial to the function of the enzyme. An electrophoretic heterogeneity within the pig heart alpha-subunit, similar to that shown by bovine subunits 3/4, was demonstrated. One reordering of the Cys-containing peptides of the pig heart alpha-subunit is indicated. Sequence comparison with the distantly related NADP(+)-dependent enzyme from Escherichia coli, for which the three-dimensional structure is known [Stoddard, Dean and Koshland (1993) Biochemistry 32, 9310-9316] shows strong conservation of residues binding isocitrate, Mg2+ and the NAD+ moiety of NADP+, consistent with a catalytic function.

Three-dimensional structure and mimetic-membrane association of consensus 11-amino-acid motif from soybean lea3 protein

Biopolymers ◽  
2011 ◽  
Vol 98 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Rong Xue ◽  
Yun Liu ◽  
Yizhi Zheng ◽  
Yijie Wu ◽  
Xiaojing Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Membrane Association ◽  
Amino Acid Motif ◽  
Three Dimensional Structure
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