Recapitulation and Design of Protein Binding Peptide Structures and Sequences

2006 ◽  
Vol 357 (3) ◽  
pp. 917-927 ◽  
Author(s):  
Vanita D. Sood ◽  
David Baker
Keyword(s):  
Protein Binding ◽  
Binding Peptide

scholarly journals Computational Design of the Sequence and Structure of a Protein-Binding Peptide

2011 ◽  
Vol 133 (12) ◽  
pp. 4190-4192 ◽  
Author(s):  
Deanne W. Sammond ◽  
Dustin E. Bosch ◽  
Glenn L. Butterfoss ◽  
Carrie Purbeck ◽  
Mischa Machius ◽  
...  
Keyword(s):  
Protein Binding ◽  
Computational Design ◽  
Binding Peptide

scholarly journals Intra-protein binding peptide fragments have specific and intrinsic sequence patterns

2017 ◽  
Author(s):  
Yuhong Wang ◽  
Junzhou Huang ◽  
Wei Li ◽  
Sheng Wang ◽  
Chuanfan Ding
Keyword(s):  
Protein Binding ◽  
Learning Algorithm ◽  
Double Helix ◽  
Peptide Fragments ◽  
Feed Forward Neural Network ◽  
Binding Peptide ◽  
Protein Protein Interaction ◽  
Deep Learning Algorithm ◽  
Sequence Patterns ◽  
Dna Double Helix

AbstractThe key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins. Here we show that similar rules and intrinsic sequence patterns between intra-protein binding peptide fragments do exist, and they can be extracted using a deep learning algorithm. Multi-millions of binding and non-binding peptide fragments from currently available protein X-ray structures are classified with an accuracy of up to 93%. This discovery has the potential in helping solve protein folding and protein-protein interaction problems, two open and fundamental problems in molecular biology.One Sentence SummaryClassification of binding and non-binding intra-protein peptide fragments using feed-forward neural network

scholarly journals Molecular mechanism of multispecific recognition of Calmodulin through conformational changes

2017 ◽  
Vol 114 (20) ◽  
pp. E3927-E3934 ◽  
Author(s):  
Fei Liu ◽  
Xiakun Chu ◽  
H. Peter Lu ◽  
Jin Wang
Keyword(s):  
Protein Binding ◽  
Conformational Change ◽  
Molecular Mechanism ◽  
Conformational Changes ◽  
Electrostatic Interaction ◽  
Hydrophobic Interaction ◽  
High Specificity ◽  
Binding Peptide ◽  
Conformational Selection ◽  
High Affinity

Calmodulin (CaM) is found to have the capability to bind multiple targets. Investigations on the association mechanism of CaM to its targets are crucial for understanding protein–protein binding and recognition. Here, we developed a structure-based model to explore the binding process between CaM and skMLCK binding peptide. We found the cooperation between nonnative electrostatic interaction and nonnative hydrophobic interaction plays an important role in nonspecific recognition between CaM and its target. We also found that the conserved hydrophobic anchors of skMLCK and binding patches of CaM are crucial for the transition from high affinity to high specificity. Furthermore, this association process involves simultaneously both local conformational change of CaM and global conformational changes of the skMLCK binding peptide. We found a landscape with a mixture of the atypical “induced fit,” the atypical “conformational selection,” and “simultaneously binding–folding,” depending on the synchronization of folding and binding. Finally, we extend our discussions on multispecific binding between CaM and its targets. These association characteristics proposed for CaM and skMLCK can provide insights into multispecific binding of CaM.

scholarly journals Identification of materials' binding peptide sequences guided by a MALDI-ToF MS depletion assay

2014 ◽  
Vol 6 (5) ◽  
pp. 1501-1509 ◽  
Author(s):  
Sascha Steckbeck ◽  
Julian Schneider ◽  
Linda Wittig ◽  
Klaus Rischka ◽  
Ingo Grunwald ◽  
...  
Keyword(s):  
Protein Binding ◽  
Md Simulations ◽  
Binding Peptide ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

This work explores the feasibility of a new MALDI-ToF MS depletion assay for the monitoring of protein binding onto surfaces and the identification of material-binding peptide sequences. The results of MALDI-ToF MS measurements are validated by HPLC, AFM, QCM-D and MD simulations.

Bone Morphogenetic Protein Binding Peptide Mechanism and Enhancement of Osteogenic Protein-1 Induced Bone Healing

Spine ◽  
2010 ◽  
Vol 35 (23) ◽  
pp. 2049-2056 ◽  
Author(s):  
Cyrus E. Taghavi ◽  
Kwang-Bok Lee ◽  
Wubing He ◽  
Gun Keorochana ◽  
Samuel S. Murray ◽  
...  
Keyword(s):  
Protein Binding ◽  
Bone Morphogenetic Protein ◽  
Bone Healing ◽  
Binding Peptide ◽  
Morphogenetic Protein ◽  
Osteogenic Protein

Can Bone Morphogenetic Protein Binding Peptide Increase Efficiency of Bone Formation?

Spine ◽  
2010 ◽  
Vol 35 (17) ◽  
pp. 1655-1659 ◽  
Author(s):  
Scott C. McGovern ◽  
Winston Fong ◽  
Jeffrey C. Wang
Keyword(s):  
Bone Formation ◽  
Protein Binding ◽  
Bone Morphogenetic Protein ◽  
Binding Peptide ◽  
Morphogenetic Protein ◽  
Increase Efficiency
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