Prediction of long-range contacts in protein tertiary structures by Soh, Lam Soon.

“…In this project, a predictor will be created to predict long range contacts in 3D protein structures. This is done by first analyzing the structural information of the protein, based on the distances, and creating a predictor using neural networks. …”
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Comparison of membrane protein modeling tools and case study on potassium ion channel by Cheong, Jennifer Sze Mun.

“…Although membrane proteins comprise one third of the human genome and interact with more than 50% of the whole set of proteins, only few hundred membrane protein structures have been resolved to date. Unlike other proteins, membrane structures proteins are stabilized through the interaction with solubilizing environments and membrane lipids. …”
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Conformational polymorphism, stability and aggregation in spider dragline silk proteins by Dicko, C, Knight, D, Kenney, J, Vollrath, F

“…Spider silk is spun in a complex and unique process, thought to depend on a hydriphobic conversion of a predominantly disordered to a β-sheet rich protein structures. To test this hypothesis we monitored the effect of cationic (DOTAC) and anionic (alkyl sulfate) detergents and of (ii) solvent polarity using a series of alcohols on the secondary structure transition in dilute solutions of native spidroin. …”

Exploring carbohydrate-peptide interactions in the gas phase: structure and selectivity in complexes of pyranosides with N-acetylphenylalanine methylamide. by Cocinero, E, Çarçabal, P, Vaden, T, Davis, B, Simons, J

“…None of the structures is supported by "stacking" interactions with the aromatic ring, despite their common occurrence in bound carbohydrate-protein structures.…”

K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations. by Furini, S, Domene, C

“…As of this writing, the relentless growth in computational power, the development of new algorithms to tackle the so-called rare events, improved force-field parameters, and the concomitant increasing availability of membrane protein structures, allow simulations to contribute even further, providing more-complete models of ion conduction and selectivity in ion channels. …”

The impact of glycosylation on the biological function and structure of human immunoglobulins. by Arnold, J, Wormald, M, Sim, R, Rudd, P, Dwek, R

“…The models were constructed by combining glycan sequencing data with oligosaccharide linkage and dynamics information from the Glycobiology Institute experimental database and protein structural data from "The Protein Data Bank."…”

Self-assembly of toroidal proteins explored using native mass spectrometry by Yewdall, N, Allison, T, Pearce, F, Robinson, C, Gerrard, J

“…This study provides the foundation for the rational design and precise characterisation of peroxiredoxin protein structures where self-assembly can be harnessed as a key feature for applications in nanotechnology.…”

Helix kinks are equally prevalent in soluble and membrane proteins by Wilman, H, Shi, J, Deane, C

“…. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.…”

Simulation-based prediction of phosphatidylinositol 4,5-bisphosphate binding to an ion channel. by Schmidt, MR, Stansfeld, P, Tucker, S, Sansom, MS

“…In addition to providing insight into the mechanism by which PIP(2) binds to Kir2.2, these results help to establish the validity of this multiscale simulation approach and its future application in the examination of novel membrane protein-lipid interactions in the increasing number of high-resolution membrane protein structures that are now available.…”

How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain. by Sands, Z, Sansom, MS

“…The nature of voltage sensing by voltage-activated ion channels is a key problem in membrane protein structural biology. The way in which the voltage-sensor (VS) domain interacts with its membrane environment remains unclear. …”

STITCHER: Dynamic assembly of likely amyloid and prion beta-structures from secondary structure predictions by Bryan, Allen W., O'Donnell, Charles William, Menke, Matthew E., Cowen, Lenore J., Lindquist, Susan, Berger Leighton, Bonnie

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Classification of protein sequences in coronavirus and other human viruses by Lee, Ryan Kai Jun

“…This remains a relevant problem in understanding how the sequence alignment of proteins relate to its protein structures in the formulation of these antiviral drugs (Tomar and Arkin 2020). …”
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Telomere biology disorders by Kam, Michelle L. W., Nguyen, Trang T. T., Ngeow, Joanne Yuen Yie

“…Telomeres are DNA-protein structures at chromosome ends that maintain chromosome stability; their length affects cell replicative potential and senescence. …”
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Accurate prediction of protein function using statistics-informed graph networks by Jang, YJ, Qin, Q, Huang, S, Peter, ATJ, Ding, X, Kornmann, B

“…However, more than 200 million proteins remain uncharacterized, and computational efforts heavily rely on protein structural information to predict annotations of varying quality. …”

Lipid-dependent regulation of ion channels and GPCRs: insights from structures and simulations by Duncan, A, Song, W, Sansom, MSP

“…Structural studies combined with biophysical and molecular simulation investigations reveal interaction sites for specific lipids on membrane protein structures. For K channels, PIP2 plays a key role in regulation of Kv and Kir channels. …”

Multifaceted approaches including neoglycolipid oligosaccharide microarrays to ligand discovery for malectin. by Palma, A, Liu, Y, Muhle-Goll, C, Butters, T, Zhang, Y, Childs, R, Chai, W, Feizi, T

“…The malectin story is an example of a powerful convergence of disciplines in biological sciences: (i) developmental biology, (ii) bioinformatics, (iii) recombinant protein expression, (iv) protein structural studies, (v) glucan biochemistry, and (vi) drug-assisted engineering of oligosaccharide biosynthesis, culminating in (vii) oligosaccharide "designer" microarrays, to clinch the remarkable selectivity of the binding of this newly discovered ER protein. …”

Protein complexes are under evolutionary selection to assemble via ordered pathways. by Marsh, J, Hernández, H, Hall, Z, Ahnert, SE, Perica, T, Robinson, C, Teichmann, SA

“…Finally, we observe protein structural constraints on the gene order of fusion that impact the potential for fusion to affect assembly. …”

A critical evaluation of the predicted and X-ray structures of alpha-lactalbumin. by Acharya, K, Stuart, D, Phillips, D, Scheraga, H

“…The rapidly increasing availability of protein amino-acid sequences, many of which have been determined from the corresponding gene sequences, has intensified interest in the prediction of related protein structures when the three-dimensional structure of another member of the family is known. …”

Polyalanine reconstruction from Calpha positions using the program CALPHA can aid initial phasing of data by molecular replacement procedures. by Esnouf, R

“…Reconstructions can be by manual rebuilding, from geometric solutions to the constraints on main-chain torsion angles or from databases of known protein structures. The last method is usually the most convenient and reliable. …”

Partially folded forms of barley lipid transfer protein are more surface active. by Clare Mills, E, Gao, C, Wilde, P, Rigby, N, Wijesinha-Bettoni, R, Johnson, V, Smith, L, Mackie, A

“…Thermal and chemical modification of protein structures is known to affect their interfacial activity. …”