Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures

Lessandra Eller; Luiz Rocha

doi:doi:10.11648/j.ijbbmb.20180302.11

| Peer-Reviewed

Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures

Lessandra Eller, Luiz Rocha

Published in International Journal of Biochemistry, Biophysics & Molecular Biology (Volume 3, Issue 2)

Received: 18 April 2018 Accepted: 8 May 2018 Published: 1 June 2018

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

Homologous proteins are special macromolecules with related primary sequences and multiple native structures and together with sequence-unrelated nonhomologous ones both constitute the protein amazing universe. Here is made a thorough sample selection, and employed quantitative predictions to analyze structures, conformations, steric and hydrophobic interactions and underlying molecular mechanisms in proteins via two coarse-grained (hydrophobic-polar, large-small) models. First, five empirical relations from nonhomologous samples are determined correlating large and hydrophobic residue sequences from primary to helix and β-sheet structures of functional conformations. When applied to homologous proteins, such empirical relations allow precisely surveying the interaction performance, identifying four types of molecular mechanisms, and computing the stability level in conformation ensembles. 1764 structural inspections capture essential features and furnish structural-interactional insights for homologous proteins, as well as suggest a fruitful way for better understanding conformational variability in biomolecular processes such as protein evolution, dynamics, folding and design.

Published in	International Journal of Biochemistry, Biophysics & Molecular Biology (Volume 3, Issue 2)
DOI	10.11648/j.ijbbmb.20180302.11
Page(s)	19-29
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2018. Published by Science Publishing Group

Keywords

Coarse-Grained Model, Conformational Ensemble, Homologous Protein, Molecular Sequence Data, Structural Homology, Sequence-Structure Alignment

References

[1]	Z. Dosztányi, C. Magyar, G. E. Tusnády, M. Cserzõ, A. Fiser, I. Simon. Servers for sequence–structure relationship analysis and prediction. Nucleic Acids Res. 31(13), 2003, 3359–3363.
[2]	D. J. Selkoe. Folding proteins in fatal ways. Nature 426, 2003, 900–904.
[3]	K. A. Dill, S. B. Ozkan, M. S. Shell, T. R. Weikl. The Protein Folding Problem. Annu. Rev. Biophys. 37, 2008, 289–316.
[4]	Z. Zhu-Qing. Folding Mechanism of De novo Designed Proteins. Acta Phys.-Chim. Sinic. 28(10), 2012, 2381–2389.
[5]	Z.-R. Xie, J. Chen, Y. Wu. A coarse-grained model for the simulations of biomolecular interactions in cellular environments. J. Chem. Phys. 140, 2014, 054112–1–12.
[6]	L. F. O. Rocha. Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications. Biochem. Mol. Biol. 2(2), 2017, 12–24.
[7]	A. G. Murzin, S. E. Brenner, T. Hubbard, C. Chothia. SCOP: A Structural Classification of the Protein Database for the Investigation of Sequences and Structures. J. Mol. Biol. 247, 1995, 536–540.
[8]	N.-K. Kim, J. Xie. Protein Multiple Alignment Incorporating Primary and Secondary Structure Information. J. Comp. Biol. 13(9), 2006, 1615–1629.
[9]	E. Krissinel. On the relationship between sequence and structure similarities in proteomics. Bioinformatics 23(6), 2007, 717–723.
[10]	Y. Wang, R. I. Sadreyev, N. V. Grishin. PROCAIN server for remote protein sequence similarity search. Bioinformatics 25(16), 2009, 2076–2077.
[11]	M. Kosloff, R. Kolodny. Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 71, 2008, 891–902.
[12]	K. Arnold, L. Bordoli, J. Kopp, T. Schwede. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22(2), 2006, 195–201.
[13]	J. Pei, B.-H. Kim, M. Tang, N. V. Grishin. PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res. 35, 2007, W649–W652.
[14]	Y.-C. Hsu, C.-M. Chen, T.-W. Pai, J.-F. Jeng, C.-H. Hu, W.-S. Tzou. Length Encoded Secondary Structure Profile for Remote Homologous Protein Detection. A. Hua, S.-L. Chang (Eds.): ICA3PP 2009, LNCS 5574, Springer-Verlag Berlin Heidelberg 2009, 1–11.
[15]	N. Echols, D. Milburn, M. Gerstein: MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31, 2003, 478–482.
[16]	M. Gerstein, N. Echols. Exploring the range of protein flexibility, from a structural proteomics perspective. Curr. Opin. Chem. Biol. 8, 2004, 14–19.
[17]	S. K. Mani, H. Balasubramanian, S. Nallusamy, S. Samuel. Sequence and structural analysis of two designed proteins with 88% identity adopting different folds. PEDS 23(12), 2010, 911–918.
[18]	C. O. Nwamba, K. Ibrahim. The Role of Protein Conformational Switches in Pharmacology: Its Implications in Metabolic Reprogramming and Protein Evolution. Cell Biochem. Biophys. 68, 2014, 455–462.
[19]	H. Berman, K. Henrick, H. Nakamura. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10(12), 2003, 980.
[20]	C. Chothia, A. M. Lesk. The relation between the divergence of sequence and structure in Proteins. EMBO J. 5(4), 1986, 823–826.
[21]	A. Baruah, P. Biswas. The role of site-directed point mutations in protein misfolding. Phys. Chem. Chem. Phys. 16, 2014, 13964–13973.
[22]	L. J. Fox. An Introduction to Mathematical Probability. Chapter 2. Human Nature, Biology, and Social Structure: A Critical Look at What Science Can Tell Us About Society. Vol. V, 1987.
[23]	E. G. Hutchinson, J. M. Thornton. PROMOTIF--A program to identify and analyze structural motifs in proteins. Protein Sci. 5, 1996, 212–220.
[24]	E. S. Huang, S. Subbiah, M. Levitt. Recognizing Native Folds by the Arrangement of Hydrophobic and Polar Residues. J. Mol. Biol. 252, 1995, 709–720.
[25]	M. Gerstein, C. Chothia. Packing at the protein-water interface. Proc. Natl. Acad. Sci. USA 93, 1996, 10167–10172.
[26]	L. F. O. Rocha, I. R. Silva, A. Caliri. Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study. Phys. A 388, 2009, 4097–4104.
[27]	A. A. Zamyatnin. Protein volume in solution. Progr. Biophys. Mol. Biol. 24, 1972, 107–123.
[28]	S. Moelbert, E. Emberly, C. Tang. Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins. Protein Sci. 13, 2004, 752–762.
[29]	L. F. O. Rocha. Toward a better understanding of structural divergences in proteins using different secondary structure assignment methods. J. Mol. Struct. 1063, 2014, 242–250.
[30]	K. H. DuBay, G. R. Bowman, P. L. Geissler. Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation. Acc. Chem. Res. 48, 2015, 1098−1105.
[31]	M. U. Hammer, T. H. Anderson, A. Chaimovich, M. S. Shell, J. Israelachvili. The search for the hydrophobic force law. Faraday Discuss. 146, 2010, 299–308.
[32]	M. M. Gromiha, S. Selvaraj. Protein secondary structure prediction in different structural classes. Protein Engng. 11(4), 1998, 249–251.
[33]	B. Wathen, J. Zongchao. A hierarchical order within protein structures underlies large separations between strands in β-sheets. Proteins 81, 2013, 163–175.
[34]	H.-C. Chung, C.-P. Han. Conditional confidence intervals for classification error rate. Comput. Statist. Dat. Analys. 53, 2009, 4358–4369.
[35]	S. Moreno-Hernández, M. Levitt. Comparative modeling and protein-like features of hydrophobic–polar models on a two-dimensional lattice. Proteins 80, 2012, 1683–1693.
[36]	W. G. Noid. Perspective: Coarse-grained models for biomolecular systems. J. Chem. Phys. 139, 2013, 090901–1–25.
[37]	J. Hu, T. Chen, M. Wang, H. S. Chan, Z. Q. Zhang. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding. Phys. Chem. Chem. Phys. 19(21), 2017, 13629–13639.
[38]	H. C. Li, Y. Y. Chang, J. Y. Lee, I. Bahar, L. W. Yang. DynOmics: dynamics of structural proteome and beyond. Nucleic Acid Res. 45(W1), 2017, W374–W380.
[39]	R. Schneider, A. de Daruvar, C. Sander. The HSSP database of protein structure–sequence alignments. Nucleic Acids Res. 25(1), 1997, 226–230.
[40]	C. Guda, L. R. Pal, I. N. Shindyalov. DMAPS: a database of multiple alignments for protein structures. Nucleic Acids Res. 34, 2006, D273–D276.
[41]	A. Zemla, B. Geisbrecht, J. Smith, M. Lam, B. Kirkpatrick, M. Wagner, T. Slezak, C. E. Zhou. STRALCP—structure alignment-based clustering of proteins. Nucleic Acids Res. 35(22), 2007, e150–1–8.
[42]	J. Pei, M. Tang, N. V. Grishin. PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res. 36, 2008, W30–W34.
[43]	R. C. Edgar. Quality measures for protein alignment benchmarks. Nucleic Acids Res. 38(7), 2010, 2145–2153.
[44]	D. Gront, M. Blaszczyk, P. Wojciechowski, A. Kolinski. BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles. Nucleic Acids Res. 40, 2012, W257–W262.
[45]	J. Wang, W. Wang. Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics. Adv. Phys.-X. 1 (3), 2016, 444–466.
[46]	R. L. Baldwin, G. D. Rose. Is protein folding hierarchic? II. Folding intermediates and transition states. TIBS 24, 1999, 77–83.
[47]	L. C. James, D. S. Tawfik. Conformational diversity and protein evolution – a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28(7), 2003, 361–368.
[48]	V. N. Uversky, A. K. Dunker. Understanding protein non-folding. Biochim. Biophys. Acta 1804, 2010, 1231–1264.
[49]	A. Perez, A. Roy, K. Kasavajhala, A. Wagaman, K. A. Dill, J. L. MacCallum. Extracting representative structures from protein conformational ensembles. Proteins 82, 2014, 2671–2680.
[50]	A. Kumar, A. Baruah, P. Biswas. Role of local and nonlocal interactions in folding and misfolding of globular proteins. J. Chem. Phys. 146 (6), 2017, 065102.
[51]	E. Ferrada. The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets. Plos Comp. Biol. 10(12), 2014, e1003946–1–20.
[52]	D. L. Shaw, A. S. M. S. Islam, M. S. Rahman, M. Hasan. Protein folding in HP model on hexagonal lattices with diagonals. BMC Bioinformatics 15 (Suppl 2), 2014, 1–13.
[53]	A. G. Citrolo, G. Mauri. A local landscape mapping method for protein structure prediction in the HP model. Nat. Comput. 13, 2014, 309–319.
[54]	T. Wüst, D. Reith, P. Virnau. Sequence Determines Degree of Knottedness in a Coarse-Grained Protein Model. Phys. Rev. Lett. 114, 2015, 028102–1–5.
[55]	C. R. Terrell, L. L. Listenberger. Using molecular visualization to explore protein structure and function and enhance student facility with computational tools. Biochem. Mol. Biol. Educ. 45(4), 2017, 318–328.
[56]	D. Vlachakis, A. Armaos, S. Kossida. Advanced Protein Alignments Based on Sequence, Structure and Hydropathy Profiles; The Paradigm of the Viral Polymerase Enzyme. Math. Comput. Sci. 11(2), 2017, 197–208.
[57]	L. F. O. Rocha. Analysis of molecular structures and mechanisms for toxins derived from venomous animals. Comput. Biol. Chem. 61, 2016, 8–14.
[58]	M. L. Hekkelman, G. Vriend. MRS: a fast and compact retrieval system for biological data. Nucleic Acids Res. 33, 2005, W766–W769.

Cite This Article

Plain Text BibTeX RIS

APA Style

Lessandra Eller, Luiz Rocha. (2018). Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures. International Journal of Biochemistry, Biophysics & Molecular Biology, 3(2), 19-29. https://doi.org/10.11648/j.ijbbmb.20180302.11

Copy | Download

ACS Style

Lessandra Eller; Luiz Rocha. Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures. Int. J. Biochem. Biophys. Mol. Biol. 2018, 3(2), 19-29. doi: 10.11648/j.ijbbmb.20180302.11

Copy | Download

AMA Style

Lessandra Eller, Luiz Rocha. Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures. Int J Biochem Biophys Mol Biol. 2018;3(2):19-29. doi: 10.11648/j.ijbbmb.20180302.11

Copy | Download

@article{10.11648/j.ijbbmb.20180302.11,
  author = {Lessandra Eller and Luiz Rocha},
  title = {Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures},
  journal = {International Journal of Biochemistry, Biophysics & Molecular Biology},
  volume = {3},
  number = {2},
  pages = {19-29},
  doi = {10.11648/j.ijbbmb.20180302.11},
  url = {https://doi.org/10.11648/j.ijbbmb.20180302.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijbbmb.20180302.11},
  abstract = {Homologous proteins are special macromolecules with related primary sequences and multiple native structures and together with sequence-unrelated nonhomologous ones both constitute the protein amazing universe. Here is made a thorough sample selection, and employed quantitative predictions to analyze structures, conformations, steric and hydrophobic interactions and underlying molecular mechanisms in proteins via two coarse-grained (hydrophobic-polar, large-small) models. First, five empirical relations from nonhomologous samples are determined correlating large and hydrophobic residue sequences from primary to helix and β-sheet structures of functional conformations. When applied to homologous proteins, such empirical relations allow precisely surveying the interaction performance, identifying four types of molecular mechanisms, and computing the stability level in conformation ensembles. 1764 structural inspections capture essential features and furnish structural-interactional insights for homologous proteins, as well as suggest a fruitful way for better understanding conformational variability in biomolecular processes such as protein evolution, dynamics, folding and design.},
 year = {2018}
}

Copy | Download

TY  - JOUR
T1  - Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures
AU  - Lessandra Eller
AU  - Luiz Rocha
Y1  - 2018/06/01
PY  - 2018
N1  - https://doi.org/10.11648/j.ijbbmb.20180302.11
DO  - 10.11648/j.ijbbmb.20180302.11
T2  - International Journal of Biochemistry, Biophysics & Molecular Biology
JF  - International Journal of Biochemistry, Biophysics & Molecular Biology
JO  - International Journal of Biochemistry, Biophysics & Molecular Biology
SP  - 19
EP  - 29
PB  - Science Publishing Group
SN  - 2575-5862
UR  - https://doi.org/10.11648/j.ijbbmb.20180302.11
AB  - Homologous proteins are special macromolecules with related primary sequences and multiple native structures and together with sequence-unrelated nonhomologous ones both constitute the protein amazing universe. Here is made a thorough sample selection, and employed quantitative predictions to analyze structures, conformations, steric and hydrophobic interactions and underlying molecular mechanisms in proteins via two coarse-grained (hydrophobic-polar, large-small) models. First, five empirical relations from nonhomologous samples are determined correlating large and hydrophobic residue sequences from primary to helix and β-sheet structures of functional conformations. When applied to homologous proteins, such empirical relations allow precisely surveying the interaction performance, identifying four types of molecular mechanisms, and computing the stability level in conformation ensembles. 1764 structural inspections capture essential features and furnish structural-interactional insights for homologous proteins, as well as suggest a fruitful way for better understanding conformational variability in biomolecular processes such as protein evolution, dynamics, folding and design.
VL  - 3
IS  - 2
ER  -

Copy | Download

Author Information

Lessandra Eller

Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences of Ribeir?o Preto, University of S?o Paulo, Ribeir?o Preto, S?o Paulo, Brazil
Luiz Rocha

Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences of Ribeir?o Preto, University of S?o Paulo, Ribeir?o Preto, S?o Paulo, Brazil

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Lessandra Eller, Luiz Rocha. (2018). Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures. International Journal of Biochemistry, Biophysics & Molecular Biology, 3(2), 19-29. https://doi.org/10.11648/j.ijbbmb.20180302.11

Copy | Download

ACS Style

Lessandra Eller; Luiz Rocha. Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures. Int. J. Biochem. Biophys. Mol. Biol. 2018, 3(2), 19-29. doi: 10.11648/j.ijbbmb.20180302.11

Copy | Download

AMA Style

Lessandra Eller, Luiz Rocha. Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures. Int J Biochem Biophys Mol Biol. 2018;3(2):19-29. doi: 10.11648/j.ijbbmb.20180302.11

Copy | Download

@article{10.11648/j.ijbbmb.20180302.11,
  author = {Lessandra Eller and Luiz Rocha},
  title = {Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures},
  journal = {International Journal of Biochemistry, Biophysics & Molecular Biology},
  volume = {3},
  number = {2},
  pages = {19-29},
  doi = {10.11648/j.ijbbmb.20180302.11},
  url = {https://doi.org/10.11648/j.ijbbmb.20180302.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijbbmb.20180302.11},
  abstract = {Homologous proteins are special macromolecules with related primary sequences and multiple native structures and together with sequence-unrelated nonhomologous ones both constitute the protein amazing universe. Here is made a thorough sample selection, and employed quantitative predictions to analyze structures, conformations, steric and hydrophobic interactions and underlying molecular mechanisms in proteins via two coarse-grained (hydrophobic-polar, large-small) models. First, five empirical relations from nonhomologous samples are determined correlating large and hydrophobic residue sequences from primary to helix and β-sheet structures of functional conformations. When applied to homologous proteins, such empirical relations allow precisely surveying the interaction performance, identifying four types of molecular mechanisms, and computing the stability level in conformation ensembles. 1764 structural inspections capture essential features and furnish structural-interactional insights for homologous proteins, as well as suggest a fruitful way for better understanding conformational variability in biomolecular processes such as protein evolution, dynamics, folding and design.},
 year = {2018}
}

Copy | Download

TY  - JOUR
T1  - Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures
AU  - Lessandra Eller
AU  - Luiz Rocha
Y1  - 2018/06/01
PY  - 2018
N1  - https://doi.org/10.11648/j.ijbbmb.20180302.11
DO  - 10.11648/j.ijbbmb.20180302.11
T2  - International Journal of Biochemistry, Biophysics & Molecular Biology
JF  - International Journal of Biochemistry, Biophysics & Molecular Biology
JO  - International Journal of Biochemistry, Biophysics & Molecular Biology
SP  - 19
EP  - 29
PB  - Science Publishing Group
SN  - 2575-5862
UR  - https://doi.org/10.11648/j.ijbbmb.20180302.11
AB  - Homologous proteins are special macromolecules with related primary sequences and multiple native structures and together with sequence-unrelated nonhomologous ones both constitute the protein amazing universe. Here is made a thorough sample selection, and employed quantitative predictions to analyze structures, conformations, steric and hydrophobic interactions and underlying molecular mechanisms in proteins via two coarse-grained (hydrophobic-polar, large-small) models. First, five empirical relations from nonhomologous samples are determined correlating large and hydrophobic residue sequences from primary to helix and β-sheet structures of functional conformations. When applied to homologous proteins, such empirical relations allow precisely surveying the interaction performance, identifying four types of molecular mechanisms, and computing the stability level in conformation ensembles. 1764 structural inspections capture essential features and furnish structural-interactional insights for homologous proteins, as well as suggest a fruitful way for better understanding conformational variability in biomolecular processes such as protein evolution, dynamics, folding and design.
VL  - 3
IS  - 2
ER  -

Copy | Download