scholarly journals Monolayer-to-thin-film transition in supramolecular assemblies: the role of topological protection

Nanoscale ◽  
2017 ◽  
Vol 9 (33) ◽  
pp. 11959-11968 ◽  
Author(s):  
Zachary P. L. Laker ◽  
Alexander J. Marsden ◽  
Oreste De Luca ◽  
Ada Della Pia ◽  
Luís M. A. Perdigão ◽  
...  
Keyword(s):  
Thin Film ◽  
Three Dimensional ◽  
Supramolecular Assemblies ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Organic Layers ◽  
Insight Into

An innovative combination of TEM and STM sheds new insight into the growth of organic layers and reveals the importance of topology in controlling the transition from two- to three-dimensional structure.

Three-dimensional structure of the buffer/absorber interface in CdS/CuGaSe2 based thin film solar cells

2009 ◽  
Vol 95 (17) ◽  
pp. 173502 ◽  
Author(s):  
M. Rusu ◽  
M. Bär ◽  
S. Lehmann ◽  
S. Sadewasser ◽  
L. Weinhardt ◽  
...  
Keyword(s):  
Thin Film ◽  
Solar Cells ◽  
Three Dimensional ◽  
Thin Film Solar Cells ◽  
Dimensional Structure ◽  
Three Dimensional Structure

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals FpvA-Mediated Ferric Pyoverdine Uptake in Pseudomonas aeruginosa: Identification of Aromatic Residues in FpvA Implicated in Ferric Pyoverdine Binding and Transport

2005 ◽  
Vol 187 (24) ◽  
pp. 8511-8515 ◽  
Author(s):  
Jiang-Sheng Shen ◽  
Valérie Geoffroy ◽  
Shadi Neshat ◽  
Zongchao Jia ◽  
Allison Meldrum ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Aromatic Residues ◽  
Three Dimensional Structure

ABSTRACT A number of aromatic residues were seen to cluster in the upper portion of the three-dimensional structure of the FpvA ferric pyoverdine receptor of Pseudomonas aeruginosa, reminiscent of the aromatic binding pocket for ferrichrome in the FhuA receptor of Escherichia coli. Alanine substitutions in three of these, W362, W391, and F795, markedly compromised ferric pyoverdine binding and transport, consistent with a role of FpvA in ferric pyoverdine recognition.

scholarly journals Architecturally complex O-glycopeptidases are customized for mucin recognition and hydrolysis

2021 ◽  
Vol 118 (10) ◽  
pp. e2019220118
Author(s):  
Benjamin Pluvinage ◽  
Elizabeth Ficko-Blean ◽  
Ilit Noach ◽  
Christopher Stuart ◽  
Nicole Thompson ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Peptide Bond ◽  
Molecular Organization ◽  
Dimensional Structure ◽  
Carbohydrate Binding ◽  
Functional Roles ◽  
Protein Substrates ◽  
Individual Domain ◽  
Insight Into

A challenge faced by peptidases is the recognition of highly diverse substrates. A feature of some peptidase families is the capacity to specifically use post-translationally added glycans present on their protein substrates as a recognition determinant. This is ultimately critical to enabling peptide bond hydrolysis. This class of enzyme is also frequently large and architecturally sophisticated. However, the molecular details underpinning glycan recognition by these O-glycopeptidases, the importance of these interactions, and the functional roles of their ancillary domains remain unclear. Here, using the Clostridium perfringens ZmpA, ZmpB, and ZmpC M60 peptidases as model proteins, we provide structural and functional insight into how these intricate proteins recognize glycans as part of catalytic and noncatalytic substrate recognition. Structural, kinetic, and mutagenic analyses support the key role of glycan recognition within the M60 domain catalytic site, though they point to ZmpA as an apparently inactive enzyme. Wider examination of the Zmp domain content reveals noncatalytic carbohydrate binding as a feature of these proteins. The complete three-dimensional structure of ZmpB provides rare insight into the overall molecular organization of a highly multimodular enzyme and reveals how the interplay of individual domain function may influence biological activity. O-glycopeptidases frequently occur in host-adapted microbes that inhabit or attack mucus layers. Therefore, we anticipate that these results will be fundamental to informing more detailed models of how the glycoproteins that are abundant in mucus are destroyed as part of pathogenic processes or liberated as energy sources during normal commensal lifestyles.

The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis

Science ◽  
1987 ◽  
Vol 237 (4817) ◽  
pp. 905-909 ◽  
Author(s):  
S Sprang ◽  
T Standing ◽  
R. Fletterick ◽  
R. Stroud ◽  
J Finer-Moore ◽  
...  
Keyword(s):  
Serine Protease ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure
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