scholarly journals De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

2000 ◽  
Vol 33 (11) ◽  
pp. 745-754 ◽  
Author(s):  
R. Blake Hill ◽  
Daniel P. Raleigh ◽  
Angela Lombardi ◽  
William F. DeGrado
Keyword(s):  
Protein Folding ◽  
Helical Bundles ◽  
And Function

ChemInform Abstract: De novo Design of Helical Bundles as Models for Understanding Protein Folding and Function

ChemInform ◽  
2001 ◽  
Vol 32 (6) ◽  
pp. no-no
Author(s):  
R. Blake Hill ◽  
Daniel P. Raleigh ◽  
Angela Lombardi ◽  
William F. Degrado
Keyword(s):  
Protein Folding ◽  
De Novo ◽  
De Novo Design ◽  
Helical Bundles ◽  
And Function

Recent successes of the energy landscape theory of protein folding and function

2005 ◽  
Vol 38 (4) ◽  
pp. 405-410 ◽  
Author(s):  
P. G. Wolynes
Keyword(s):  
Protein Folding ◽  
Energy Landscape ◽  
Helical Bundles ◽  
Energy Landscape Theory ◽  
Landscape Theory ◽  
Hydrophilic Residues ◽  
And Function ◽  
Quality Of Structure

Protein folding and binding can be understood using energy landscape theory. When seeming deviations from the predictions of the funnel hypothesis are found, landscape theory helps us locate the cause. Sometimes the deviation reflects symmetry effects, allowing extra degeneracies to occur. Such effects seem to explain some kinetic anomalies in helical bundles. When binding processes were found to use apparently non-funneled landscapes this was traced to an inadequate understanding of biomolecular forces. The discrepancy allowed the discovery of new water-mediated forces – some of which act between hydrophilic residues. Introducing such forces into the algorithms greatly improves the quality of structure predictions.

Robustness and generalization of structure-based models for protein folding and function

2009 ◽  
Vol 77 (4) ◽  
pp. 881-891 ◽  
Author(s):  
Heiko Lammert ◽  
Alexander Schug ◽  
José N. Onuchic
Keyword(s):  
Protein Folding ◽  
And Function

Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function

2018 ◽  
Vol 46 (4) ◽  
pp. 937-944 ◽  
Author(s):  
Robert Rauscher ◽  
Zoya Ignatova
Keyword(s):  
Protein Folding ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Synonymous Mutations ◽  
Translation Velocity ◽  
Disease Penetrance ◽  
And Function ◽  
Related Proteins ◽  
Translational Speed ◽  
Fine Tune

Ribosomes translate mRNAs with non-uniform speed. Translation velocity patterns are a conserved feature of mRNA and have evolved to fine-tune protein folding, expression and function. Synonymous single-nucleotide polymorphisms (sSNPs) that alter programmed translational speed affect expression and function of the encoded protein. Synergistic advances in next-generation sequencing have led to the identification of sSNPs associated with disease penetrance. Here, we draw on studies with disease-related proteins to enhance our understanding of mechanistic contributions of sSNPs to functional alterations of the encoded protein. We emphasize the importance of identification of sSNPs along with disease-causing mutations to understand genotype–phenotype relationships.

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 Familial Parkinson's Disease-associated L166P Mutation Disrupts DJ-1 Protein Folding and Function

2003 ◽  
Vol 279 (9) ◽  
pp. 8506-8515 ◽  
Author(s):  
James A. Olzmann ◽  
Keith Brown ◽  
Keith D. Wilkinson ◽  
Howard D. Rees ◽  
Qing Huai ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Protein Folding ◽  
And Function ◽  
Familial Parkinson’S Disease

scholarly journals Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport

2017 ◽  
Vol 372 (1726) ◽  
pp. 20160214 ◽  
Author(s):  
Nathan H. Joh ◽  
Gevorg Grigoryan ◽  
Yibing Wu ◽  
William F. DeGrado
Keyword(s):  
Protein Folding ◽  
Membrane Protein ◽  
Protein Design ◽  
De Novo ◽  
Cell Signalling ◽  
Membrane Protein Folding ◽  
Cellular Processes ◽  
Membrane Pores ◽  
Self Assembling ◽  
And Function

Ion transporters and channels are able to identify and act on specific substrates among myriads of ions and molecules critical to cellular processes, such as homeostasis, cell signalling, nutrient influx and drug efflux. Recently, we designed Rocker, a minimalist model for Zn 2+ /H + co-transport. The success of this effort suggests that de novo membrane protein design has now come of age so as to serve a key approach towards probing the determinants of membrane protein folding, assembly and function. Here, we review general principles that can be used to design membrane proteins, with particular reference to helical assemblies with transport function. We also provide new functional and NMR data that probe the dynamic mechanism of conduction through Rocker. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.

Compound Heterozygous Mutations Affect Protein Folding and Function in Patients With Congenital Sucrase-Isomaltase Deficiency

2009 ◽  
Vol 136 (3) ◽  
pp. 883-892 ◽  
Author(s):  
Marwan Alfalah ◽  
Markus Keiser ◽  
Tosso Leeb ◽  
Klaus–Peter Zimmer ◽  
Hassan Y. Naim
Keyword(s):  
Protein Folding ◽  
Compound Heterozygous ◽  
Compound Heterozygous Mutations ◽  
And Function
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