Host−Guest Study of Left-Handed Polyproline II Helix Formation†

Biochemistry ◽  
2001 ◽  
Vol 40 (48) ◽  
pp. 14376-14383 ◽  
Author(s):  
Melissa A. Kelly ◽  
Brian W. Chellgren ◽  
Adam L. Rucker ◽  
Jerry M. Troutman ◽  
Michael G. Fried ◽  
...  
Keyword(s):  
Helix Formation ◽  
Left Handed ◽  
Polyproline Ii ◽  
Polyproline Ii Helix

Host-guest scale of left-handed polyproline II helix formation

2003 ◽  
Vol 53 (1) ◽  
pp. 68-75 ◽  
Author(s):  
Adam L. Rucker ◽  
Cara T. Pager ◽  
Margaret N. Campbell ◽  
Joseph E. Qualls ◽  
Trevor P. Creamer
Keyword(s):  
Helix Formation ◽  
Left Handed ◽  
Polyproline Ii ◽  
Polyproline Ii Helix

scholarly journals Left-handed polyproline-II helix revisited: proteins causing proteopathies

2016 ◽  
Vol 35 (12) ◽  
pp. 2701-2713 ◽  
Author(s):  
Alexei A. Adzhubei ◽  
Anastasia A. Anashkina ◽  
Alexander A. Makarov
Keyword(s):  
Left Handed ◽  
Polyproline Ii ◽  
Polyproline Ii Helix

scholarly journals Microsecond and nanosecond polyproline II helix formation in aqueous nanodrops measured by mass spectrometry

2016 ◽  
Vol 52 (82) ◽  
pp. 12218-12221 ◽  
Author(s):  
Daniel N. Mortensen ◽  
Evan R. Williams
Keyword(s):  
Mass Spectrometry ◽  
Time Constants ◽  
Rapid Mixing ◽  
Helix Formation ◽  
Polyproline Ii ◽  
Polyproline Ii Helix

The 1.5 μs and <400 ns time constants for the formation of polyproline II helix structures in 21 and 16 residue peptides, respectively, are measured using rapid mixing from theta-glass emitters coupled with mass spectrometry.

Polyproline II Helix as a Recognition Motif of Plant Peptide Hormones and Flagellin Peptide flg22

2019 ◽  
Vol 26 (9) ◽  
pp. 684-690
Author(s):  
Norio Matsushima ◽  
Hiroki Miyashita ◽  
Shinsuke Tamaki ◽  
Robert H. Kretsinger
Keyword(s):  
Bound States ◽  
Peptide Hormones ◽  
Structural Features ◽  
Small Peptides ◽  
Left Handed ◽  
Polyproline Ii ◽  
Polyproline Ii Helix ◽  
Signaling Peptides ◽  
Leucine Rich Repeats ◽  
Atomic Coordinates

Background: Plant peptide hormones play a crucial role in plant growth and development. A group of these peptide hormones are signaling peptides with 5 - 23 amino acids. Flagellin peptide (flg22) also elicits an immune response in plants. The functions are expressed through recognition of the peptide hormones and flg22. This recognition relies on membrane localized receptor kinases with extracellular leucine rich repeats (LRR-RKs). The structures of plant peptide hormones - AtPep1, IDA, IDL1, RGFs 1- 3, TDIF/CLE41 - and of flg22 complexed with LRR domains of corresponding LRRRKs and co-receptors SERKs have been determined. However, their structures are well not analyzed and characterized in detail. The structures of PIP, CEP, CIF, and HypSys are still unknown. Objective: Our motivation is to clarify structural features of these plant, small peptides and Flg22 in their bound states. Methods: In this article, we performed secondary structure assignments and HELFIT analyses (calculating helix axis, pitch, radius, residues per turn, and handedness) based on the atomic coordinates from the crystal structures of AtPep1, IDA, IDL1, RGFs 1- 3, TDIF/CLE41 - and of flg22. We also performed sequence analysis of the families of PIP, CEP, CIF, and HypSys in order to predict their secondary structures. Results: Following AtPep1 with 23 residues adopts two left handed polyproline helices (PPIIs) with six and four residues. IDA, IDL1, RGFs 1 - 2, and TDIF/CLE41 with 12 or 13 residues adopt a four residue PPII; RGF3 adopts two PPIIs with four residues. Flg22 with 22 residues also adopts a six residue PPII. The other peptide hormones – PIP, CEP, CIF, and HypSys – that are rich in proline or hydroxyproline presumably prefer PPII. Conclusion: The present analysis indicates that PPII helix in the plant small peptide hormones and in flg22 is crucial for recognition of the LRR domains in receptors.

Urea Promotes Polyproline II Helix Formation:  Implications for Protein Denatured States†

Biochemistry ◽  
2005 ◽  
Vol 44 (16) ◽  
pp. 6269-6275 ◽  
Author(s):  
Shelly J. Whittington ◽  
Brian W. Chellgren ◽  
Veronique M. Hermann ◽  
Trevor P. Creamer
Keyword(s):  
Helix Formation ◽  
Polyproline Ii ◽  
Polyproline Ii Helix ◽  
Denatured States

scholarly journals Prediction of polyproline II secondary structure propensity in proteins

2020 ◽  
Vol 7 (1) ◽  
pp. 191239 ◽  
Author(s):  
Kevin T. O’Brien ◽  
Catherine Mooney ◽  
Cyril Lopez ◽  
Gianluca Pollastri ◽  
Denis C. Shields
Keyword(s):  
Secondary Structure ◽  
Large Scale ◽  
External Validation ◽  
Three Dimensional ◽  
Binding Domains ◽  
Left Handed ◽  
Polyproline Ii ◽  
Polyproline Ii Helix ◽  
Binding Peptides ◽  
Validation Set

Background: The polyproline II helix (PPIIH) is an extended protein left-handed secondary structure that usually but not necessarily involves prolines. Short PPIIHs are frequently, but not exclusively, found in disordered protein regions, where they may interact with peptide-binding domains. However, no readily usable software is available to predict this state. Results: We developed PPIIPRED to predict polyproline II helix secondary structure from protein sequences, using bidirectional recurrent neural networks trained on known three-dimensional structures with dihedral angle filtering. The performance of the method was evaluated in an external validation set. In addition to proline, PPIIPRED favours amino acids whose side chains extend from the backbone (Leu, Met, Lys, Arg, Glu, Gln), as well as Ala and Val. Utility for individual residue predictions is restricted by the rarity of the PPIIH feature compared to structurally common features. Conclusion: The software, available at http://bioware.ucd.ie/PPIIPRED , is useful in large-scale studies, such as evolutionary analyses of PPIIH, or computationally reducing large datasets of candidate binding peptides for further experimental validation.

scholarly journals Allosteric Modulation of the Dopamine D2Receptor by Pro-Leu-Gly-NH2Peptidomimetics Constrained in Either a Polyproline II Helix or a Type II β-Turn Conformation

2009 ◽  
Vol 52 (7) ◽  
pp. 2043-2051 ◽  
Author(s):  
Bhooma Raghavan ◽  
Kevin J. Skoblenick ◽  
Swapna Bhagwanth ◽  
Niran Argintaru ◽  
Ram K. Mishra ◽  
...  
Keyword(s):  
Allosteric Modulation ◽  
Type Ii ◽  
Polyproline Ii ◽  
Polyproline Ii Helix

Polyproline II Helix Is a Key Structural Motif of the Elastic PEVK Segment of Titin

Biochemistry ◽  
2001 ◽  
Vol 40 (12) ◽  
pp. 3427-3438 ◽  
Author(s):  
Kan Ma ◽  
Lou-sing Kan ◽  
Kuan Wang
Keyword(s):  
Structural Motif ◽  
Polyproline Ii ◽  
Polyproline Ii Helix
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