scholarly journals The Importance of Hydrogen Bonding between the Glutamine Side Chains to the Formation of Amyloid VQIVYK Parallel β-Sheets: An ONIOM DFT/AM1 Study

2010 ◽  
Vol 132 (6) ◽  
pp. 1758-1759 ◽  
Author(s):  
Joshua A. Plumley ◽  
J. J. Dannenberg
Keyword(s):  
Hydrogen Bonding ◽  
Side Chains ◽  
Β Sheets

Amyloid structure

2014 ◽  
Vol 56 ◽  
pp. 1-10 ◽  
Author(s):  
Louise Serpell
Keyword(s):  
Hydrogen Bonding ◽  
Sequence Homology ◽  
Amyloid Fibrils ◽  
Side Chains ◽  
Primary Sequence ◽  
Sheet Structure ◽  
Β Sheets ◽  
The Stability ◽  
Β Sheet ◽  
Proteins And Peptides

Amyloid fibrils are formed by numerous proteins and peptides that share little sequence homology. The structures formed are highly ordered and extremely stable, being composed of β-sheet structure and stabilized along their length by hydrogen bonding. The fibrils are formed by several protofilaments that wind around one another in rope-like structures, lending further strength and stability to the resulting fibres. The fact that so many proteins and peptides form amyloid structures under suitable conditions, seems to suggest that the sequence of the precursor is unimportant. However, it is now clear that side chains play a central role in forming interactions between several β-sheets to further stabilize and regulate the structures. The primary sequence plays a central role in determining the rate of fibril formation, the stability of the resulting structure to degradation and the final morphology of the fibrils. The side chains regulate the elongation and growth, and also the lateral association of the protofilament and fibrils, having a significant impact on the final architecture.

STRUCTURAL INSIGHT INTO THE POLYMORPHISM OF NNQNTF PROTOFIBRIL: IMPORTANCE OF INTERFACIAL WATER, POLAR AND AROMATIC RESIDUES

2013 ◽  
Vol 12 (08) ◽  
pp. 1341012
Author(s):  
YAN LU ◽  
WENHUI XI ◽  
GUANGHONG WEI
Keyword(s):  
Hydrogen Bonding ◽  
Amyloid Fibrils ◽  
Md Simulations ◽  
Side Chains ◽  
Face To Face ◽  
Recent Experimental Study ◽  
Aromatic Stacking ◽  
Detailed Structural Analysis ◽  
Physical Interactions ◽  
Β Sheets

Polymorphism is widely observed in amyloid fibrils associated with many neurodegenerative diseases. Recent experimental study reported that fibrils formed by the segment NNQNTF of elk prion protein exhibited facial polymorphism with the two β-sheets either in back-to-back (BB) or in face-to-face (FF) packing arrangement. In the BB packing, the side chains of N2, N4 and F6 are interdigitated to form steric zipper, while in the FF packing, the side chains of N1, Q3 and T5 form the interdigitated interface. In this study, we investigate the water-mediated assembly of two preformed β-sheets and the physical interactions that stabilize the two different fibrils using all-atom molecular dynamics (MD) simulations. Multiple MD simulations have been carried out by starting from FF or BB packing of two β-sheets according to the facial polymorphism revealed by X-ray microcrystallography. For both packing patterns, we observe that the assembly of β-sheets is mediated by water molecules in the interface between β-sheets, leading to a long-lived protofibrils with wet interface prior to the formation of dry amyloid fibrils. Detailed structural analysis shows that besides the side chain steric zipper interactions, intra-sheet hydrogen bonding and aromatic stacking interactions play an important role on the stabilization of the protofibril with BB packing, while the intra-sheet and inter-sheet hydrogen bonding interactions are crucial for the formation of BB protofibril. These findings provide insights into the mechanism that lead to the facial polymorphism of NNQNTF fibrils.

scholarly journals Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide

RSC Advances ◽  
2017 ◽  
Vol 7 (45) ◽  
pp. 27981-27991 ◽  
Author(s):  
Kinshuk Raj Srivastava ◽  
Bhupesh Goyal ◽  
Anil Kumar ◽  
Susheel Durani
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Mechanism ◽  
Electrostatic Interactions ◽  
Side Chains ◽  
Β Sheets ◽  
Conformational Ordering ◽  
Polypeptide Chains

The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.

Charge-Separated Fmoc-Peptide β-Sheets: Sequence-Secondary Structure Relationship for Arranging Charged Side Chains on Both Sides

2014 ◽  
Vol 3 (11) ◽  
pp. 1182-1188 ◽  
Author(s):  
Toru Nakayama ◽  
Taro Sakuraba ◽  
Shunsuke Tomita ◽  
Akira Kaneko ◽  
Eisuke Takai ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Side Chains ◽  
Structure Relationship ◽  
Β Sheets

Poly(phenylenevinylene) analogs with ring substituted polar side chains and their use in the formation of hydrogen bonding basedself-assembled multilayers

1998 ◽  
Vol 8 (4) ◽  
pp. 919-924 ◽  
Author(s):  
Iris Benjamin ◽  
Haiping Hong ◽  
Yair Avny ◽  
Dan Davidov ◽  
Ronny Neumann
Keyword(s):  
Hydrogen Bonding ◽  
Side Chains

NMR structure of bucandin, a neurotoxin from the venom of the Malayan krait (Bungarus candidus)

2001 ◽  
Vol 360 (3) ◽  
pp. 539-548 ◽  
Author(s):  
Allan M. TORRES ◽  
R. Manjunatha KINI ◽  
Nirthanan SELVANAYAGAM ◽  
Philip W. KUCHEL
Keyword(s):  
Solution Structure ◽  
Pharmacological Action ◽  
Nmr Structure ◽  
Side Chains ◽  
X Ray ◽  
Nmr Study ◽  
C Terminus ◽  
Mean Structure ◽  
Β Sheets ◽  
Β Sheet

A high-resolution solution structure of bucandin, a neurotoxin from Malayan krait (Bungarus candidus), was determined by 1H-NMR spectroscopy and molecular dynamics. The average backbone root-mean-square deviation for the 20 calculated structures and the mean structure is 0.47 Å (1 Å = 0.1nm) for all residues and 0.24 Å for the well-defined region that spans residues 23–58. Secondary-structural elements include two antiparallel β-sheets characterized by two and four strands. According to recent X-ray analysis, bucandin adopts a typical three-finger loop motif and yet it has some peculiar characteristics that set it apart from other common α-neurotoxins. The presence of a fourth strand in the second antiparallel β-sheet had not been observed before in three-finger toxins, and this feature was well represented in the NMR structure. Although the overall fold of the NMR structure is similar to that of the X-ray crystal structure, there are significant differences between the two structures that have implications for the pharmacological action of the toxin. These include the extent of the β-sheets, the conformation of the region spanning residues 42–49 and the orientation of some side chains. In comparison with the X-ray structure, the NMR structure shows that the hydrophobic side chains of Trp27 and Trp36 are stacked together and are orientated towards the tip of the middle loop. The NMR study also showed that the two-stranded β-sheet incorporated in the first loop, as defined by residues 1–22, and the C-terminus from Asn59, is probably flexible relative to the rest of the molecule. On the basis of the dispositions of the hydrophobic and hydrophilic side chains, the structure of bucandin is clearly different from those of cytotoxins.

scholarly journals Recognition of Nucleic Acid Bases and Base-pairs by Hydrogen Bonding to Amino Acid Side-chains

2003 ◽  
Vol 327 (4) ◽  
pp. 781-796 ◽  
Author(s):  
Alan C. Cheng ◽  
William W. Chen ◽  
Cynthia N. Fuhrmann ◽  
Alan D. Frankel
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Nucleic Acid ◽  
Side Chains ◽  
Nucleic Acid Bases ◽  
Base Pairs ◽  
Amino Acid Side Chains
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