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Discovering side-chain correlation in alpha-helices

T M Klingler, D L Brutlag
1994 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
The sequence correlations we find represent physical and chemical interactions among amino-acid side chains in helical structures.  ...  Lastly, we have also detect correlations in side-chain comformations that indicate important structural interactions but which don't appear as sequence correlations.  ...  Acknowledgments This work is supported in part by the CAMIS grant from the National Library of Medicine LM05305 and in part by a seed grant from the Stanford Office of Technology Licensing. Tod M.  ... 
pmid:7584396 fatcat:phvv23st3zhi5mtxqbjsa5epla

The Influence of Amino Acid Sequence on Protein Structure

Anthony V. Guzzo
1965 Biophysical Journal  
On the basis of the known sequences and structures of myoglobin, and alpha and beta hemoglobin, a possible correlation between certain amino acids in the sequence and the location of the helical and non-helical  ...  Additional support for this correlation is obtained from analyses of proline replacement in mutant and variant proteins.  ...  The polar nature of the side chain is thought to attract and orient the water atmosphere in the vicinity of the backbone chain. of the protein-the lengths of the "necessary" alpha helical sections, that  ... 
doi:10.1016/s0006-3495(65)86753-4 pmid:5884309 pmcid:PMC1367904 fatcat:znlgamcbavgmhpm3oyshfmqk4e

A Hydrogen Bond Surrogate Approach for Stabilization of Short Peptide Sequences in α-Helical Conformation

Anupam Patgiri, Andrea L. Jochim, Paramjit S. Arora
2008 Accounts of Chemical Research  
This Account describes our efforts in developing a general approach for constraining short peptides in alpha-helical conformations by a main-chain hydrogen bond surrogate (HBS) strategy.  ...  Extensive conformational analysis of HBS alpha-helices with 2D NMR, circular dichroism spectroscopies and X-ray crystallography confirms the alpha-helical structure in these compounds.  ...  or remove important side-chain FIGURE 2.  ... 
doi:10.1021/ar700264k pmid:18630933 pmcid:PMC7189275 fatcat:ctrcqclnb5enrhifm6cr5n5iaq

Protein Structure Prediction

2008 Biophysical Journal  
This discovered correlation can be described by a linear regression function.  ...  There are several other residues besides prolines that are also known to cause kinks because of the hydrogen bond between the side chains and the main chain of the helix at residues like Ser, Thr, Asn,  ...  This discovered correlation can be described by a linear regression function.  ... 
doi:10.1016/s0006-3495(08)79195-1 fatcat:qtesabyxyfhmzbzksaw4qeljga

Refinement of the main chain directed assignment strategy for the analysis of 1H NMR spectra of proteins

A.J. Wand, S.J. Nelson
1991 Biophysical Journal  
The underlying basis of the main chain directed (MCD) resonance assignment strategy for the analysis of 1H NMR spectra of proteins is reexamined.  ...  The criteria used in the construction of the patterns used in the MCD method have been extended to increase the robustness of the approach to the presence of variable protein secondary structure and significant  ...  Though taking a completely different approach it is not expected to eliminate the need for side chain spin system identification in J-correlated spectra.  ... 
doi:10.1016/s0006-3495(91)82325-6 pmid:1868155 pmcid:PMC1281345 fatcat:bkmny4aanrap7bdvolbnstmhne

Thermal stability of chicken brain α-spectrin repeat 17: a spectroscopic study

Annette K. Brenner, Bruno Kieffer, Gilles Travé, Nils Åge Frøystein, Arnt J. Raae
2012 Journal of Biomolecular NMR  
Spectrin alpha-chain Spectrin alpha-chain Spectrin alpha-chain Spectrin alpha-chain Spectrin alpha-chain Spectrin alpha-chain Spectrin alpha-chain Spectrin alpha-chain Spectrin alpha-chain Spectrin  ...  Note that backbone-side chain and side chain-side chain NOE-connectivities which are present in all types of secondary structures are not shown.  ...  Overview of important experiments The nuclei that are observed in the experiments which are described in chapter 2 are listed in table A.1 [60] .  ... 
doi:10.1007/s10858-012-9620-y pmid:22569754 fatcat:djhuzttdc5bmxcnx37t7cbk5xy

Synthetic model proteins. Positional effects of interchain hydrophobic interactions on stability of two-stranded alpha-helical coiled-coils

N E Zhou, C M Kay, R S Hodges
1992 Journal of Biological Chemistry  
We have designed a model protein that consists of two identical 35-residue polypeptide chains, parallel and in-register arranged in a two-stranded alpha-helical coiled-coil structure.  ...  All these proteins formed two-stranded alpha-helical coiled-coils in benign conditions (0.05 M phosphate, 0.1 M KCl, pH 7).  ...  Semchuk and Bob Luty for their skilled technical assistance in synthesis and purification of peptides and performing circular dichroism measurements.  ... 
pmid:1733963 fatcat:65youfobbvfgblubhi2uqvvvci

Monitoring Dimerization of GpA using FRET

Jennifer K. Binder, Sandip Shinde, Brian Woodrum, Giovanna Ghirlanda, Marcia Levitus
2012 Biophysical Journal  
By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ...  In order to demonstrate the practicality of this method, a cysteine mutated nitroxide spin label is positioned 1, 2, 3 and 4 residues away from two types of deuterated Leu side chains (denoted iþ1 to iþ4  ...  By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ... 
doi:10.1016/j.bpj.2011.11.1467 fatcat:bn5iqssv6zagnh3bpomp3hu3da

Membrane Protein Secondary Structure Determination via Pulsed EPR ESEEM

You Zhou, Shadi Abu-Baker, Lishan Liu, Indra D. Sahu, Robert M. McCarrick, Gary A. Lorigan
2012 Biophysical Journal  
By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ...  In order to demonstrate the practicality of this method, a cysteine mutated nitroxide spin label is positioned 1, 2, 3 and 4 residues away from two types of deuterated Leu side chains (denoted iþ1 to iþ4  ...  By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ... 
doi:10.1016/j.bpj.2011.11.1468 fatcat:nbshc6t2v5abzo7atiedz6dqx4

Control of Transverse Position of the Notch Transmembrane Helix by Amino Acid Sequence: Effect on γ-Secretase Mediated Cleavage and Activity of Notch

Diya Bhattacharjee, Erwin London
2012 Biophysical Journal  
By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ...  In order to demonstrate the practicality of this method, a cysteine mutated nitroxide spin label is positioned 1, 2, 3 and 4 residues away from two types of deuterated Leu side chains (denoted iþ1 to iþ4  ...  By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ... 
doi:10.1016/j.bpj.2011.11.1471 fatcat:imrcg5u5rjd7rn6unrwvaxorvy

Probing the Secondary Structure of Membrane Proteins with the Pulsed EPR ESSEM Technique

Lishan Liu, Dan Mayo, Indra Sahu, Robert McCarrick, Kaylee Troxel, Gary Lorigan
2012 Biophysical Journal  
By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ...  In order to demonstrate the practicality of this method, a cysteine mutated nitroxide spin label is positioned 1, 2, 3 and 4 residues away from two types of deuterated Leu side chains (denoted iþ1 to iþ4  ...  By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ... 
doi:10.1016/j.bpj.2011.11.1469 fatcat:6bi6z275izhvzogx26m3txhsku

The Allosteric Modulation of Syntaxin 1A by Munc18: Characterization of the Open and Closed Conformations of Syntaxin

Damian Dawidowski, David S. Cafiso
2012 Biophysical Journal  
By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ...  In order to demonstrate the practicality of this method, a cysteine mutated nitroxide spin label is positioned 1, 2, 3 and 4 residues away from two types of deuterated Leu side chains (denoted iþ1 to iþ4  ...  By using Leu instead of Val, only iþ2 and iþ3 become critical to distinguish alpha helical structure. Also, due to the longer side chain of Leu when compared to Val, 2 H modulation depth is enhanced.  ... 
doi:10.1016/j.bpj.2011.11.1470 fatcat:bcufspqr2zfappfhw53insyelu

Helix propensities of short peptides: Molecular dynamics versus bioinformatics

Christopher Bystroff, Shekhar Garde
2003 Proteins: Structure, Function, and Bioinformatics  
in the protein.  ...  The resulting trajectories were tested for reproducibility, and the helical content was measured.  ...  Position 3 prefers hydrophobic side-chains and position 5, polar side-chains.  ... 
doi:10.1002/prot.10252 pmid:12577261 fatcat:74diualejjfl7hkh53puoeeux4

Genetic Heterogeneity of Collagens

Robert E. Burgeson
1982 Journal of Investigative Dermatology  
The first class includes collagens Type I, II, and III which form classically described compact banded film struc tures resulting from crosslink stabilized side-by-side in teractions of the triple helical  ...  The third class of collagens contains the Type V colla gens and the molecules containing the E and F chains found in cartilage.  ...  , in triple-helical conformation with a second alpha chain described as a2(IV).  ... 
doi:10.1038/jid.1982.6 fatcat:ef2az3crd5dezfyjlk5tjg7bg4

Intertwined Coil Inspired Modeling of β-Barrel Membrane Protein Structures using Predicted Interstrand Interaction Constraints

Hammad Naveed, Yun Xu, Ronald Jackups, Jie Liang
2011 Biophysical Journal  
Motifs such as GG4 in alpha-helical membrane proteins and AY2 in beta-barrel membrane proteins are well recognized.  ...  We have discovered several significant motifs, (V/I/L)x(V/I/L)x(A/G) along with five others occurs in approximately 70% of the beta-strands.  ...  Motifs such as GG4 in alpha-helical membrane proteins and AY2 in beta-barrel membrane proteins are well recognized.  ... 
doi:10.1016/j.bpj.2010.12.1335 fatcat:wa3ghymqivfbjl2kv72jwch4sq
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