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Orientation sessions Sept 29 Oct 2, 6, 9, 13, 16, 20, 23, 27, 30 2017


New publications: http://www.springer.com/us/book/9783319200972 Congratulations to Authors and Springer with a year anniversary of our book: 11 Chapters. 18 Authors. More than a year of work. Thank you all.
Link to Book Home Page

New publications: Helical Assemblies: Structure Determinants. Journalof Theoretical Biology.Collaboration: The School of Theoretical Modeling and Clinical Center/NIH




Protein Models. Protein Modeling
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Chiral Assemblies
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Mutations in Uridine diphosphate N-Acetylglucoseamine 2-epimerase/N-acetylmannoseamine kinase involved in hereditary inclusion body myopathy (HIBM)

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Conformational Changes in Fibrin/Fibrinogen

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New topics in Protein Modeling

Chiral Assemblies Helical Repeats Structure Alignment

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Course Cost:
Semester course - $1,400
(10 HOURS) - $350.00
( 4 HOURS) - $180.00

     PROTEIN MODELING  ONE DAY COURSE


 9:30-10:00   Organizing procedures

     Introduction of all participants

     Short introduction to the topics of the course

10-10:55

 

Protein conformation

     Parameters characterizing polypeptide chain

     Topology, orientation of protein secondary structure elements

 

11-11:55

 

New mathematical approaches to protein structure prediction/protein modeling

     Formula for spatial location of amino acid residues within secondary structure

     elements

     Application to the prediction of protein structure

     Algorithms

 

12-1:00

 

     Lunch

 

1-1:55

 

Description of helix-helix interfaces, active sites

     Structure comparison

     Specific side chain interactions

     Amino acid composition of helix-helix interfaces

     Variations among homologs and mutagenesis

     Disulfide bonds

Representing molecular forces affecting protein folding

Modeling of loops

Protein - nucleic acid interactions

 

2-2:55

 

Agonist/antagonist affects on binding sites

Conformational changes

Formation of channels

 

3-3:55

 

Application of modeling to the analysis of the protein families involved in desease pathogenesis

 

4-4:30

 

Organizing procedures

     Summarizing questions

     Concluding remarks

 

Course is supplemented by a text book and CD with examples

Course participants are welcome to suggest topics of individual (group) interest during registration (For each session or following course discussions and practical applications)  

 
 
 

BIOGRAPHICAL INFORMATION

 


Natalya Kurochkina received her Ph.D. in Physical and Mathematical Sciences (Biophysics) in October 1990 from the Institute of Protein Research/Institute of Biophysics, Pushchino, Russian Academy of Sciences. She worked as NIH Visiting Fellow in the Laboratory of Molecular Biology of the National Cancer Institute, National Institutes of Health in Bethesda, Maryland from 1991 to 1996. After that she had a position as a Research Scientist at Applied Thermodynamics in Hunt Valley, Maryland from 1996 to 1998. Currently N.A.Kurochkina is working as Director of a School of Theoretical Modeling, Chevy Chase, Maryland. She is a member of Biophysical Society, American Association for the Advancement of Science. During this time she was working on development of methods for interpretation of electron density maps at high atomic resolution, molecular cartography, analysis of conformations with interpeptide ionic bridges, computer modeling of the process of translocation of proteins via membrane, simulation of the process of folding for peptides and proteins using Monte Carlo methods, development of hydrophobic potential based on pair-wise surface area sum for the estimation of nonpolar groups contribution in the process of folding, method for the prediction of topology for two topological groups of the four- helix bundle motif, design of antibodies with new properties, analysis of heterogeneity of packing, development of a model of protein channel, studies of conformational changes and exposure of epitopes in fibrin. Recent publications describe formula for spatial location of amino acids within secondary structure elements and its application to the prediction of protein structure, regularities in fragmentation of protein interior with respect to signal transduction, similarities found for the family of proteins with leucine repeats.

 



                                                                    All Rights Reserved  
SELECTED PUBLICATIONS

   Kurochkina, N., Iadarola M. (2015) SH Domains and Helical Assemblies. In: SH Domains. Structure, mechanisms, and applications.  Ed: Kurochkina. Springer, 2015.

   Kurochkina, N., Guha, U., Lu, Z. (2015) SH Domains and Epidermal Growth Factor Receptors. In: SH Domains. Structure, mechanisms, and applications.  Ed: Kurochkina. Springer, 2015.

    Kurochkina N, Iadarola M (2015) Helical Assemblies:Structure determinants. J Theor Biol 369C 80_84. http://dx.doi.org/10.1016/j.jtbi.2015.01.012

    Kurochkina, N., Guha, U. (2013) SH3 domains: modules of protein-protein interactions. Biophysical Reviews 5, 29-39. DOI: 10.1007/s12551-012-0081-z

   Yardeni T, Jacobs K, Niethamer TK, Ciccone C, Anikster Y, Kurochkina N, Gahl WA, Huizing M.Murine isoforms of UDP-GlcNAc 2-epimerase/ManNAc kinase: Secondary structures, expression profiles, and response to ManNAc therapy. Glycoconj J. 2012 Dec 25. [Epub ahead of print]

     Yardeni T, Choekyi T, Jacobs K, Ciccone C, Patzel K, Anikster Y, Gahl WA, Kurochkina N, Huizing M (2011) 1. Identification, Tissue Distribution, and Molecular Modeling of Novel Human Isoforms of the Key Enzyme in Sialic Acid Synthesis, UDP-GlcNAc 2-Epimerase/ManNAc Kinase. Biochemistry, 50, 8914

     N. Kurochkina, T. Choekyi. Helix-helix interfaces and ligand binding. J. Theoretical Biology (2011 )283, 92. 

     Kurochkina, N. (2011) Common structural characteristics of fibrous and globular proteins. In: Protein Structure. Ed: L. M. Haggerty. Nova Science Publishers, Inc.

     Kurochkina, Natalya & Choekyi, Tsering (2010, December 24). Helix-helix interactions of proteins involved in the process of apoptosis. SciTopics. Retrieved February 15, 2011, from http://www.scitopics.com/Helix_helix_interactions_of_proteins_involved_in_the_process_of_apoptosis.html

     N. Kurochkina. Proteins motifs and protein assemblies: role of helix-helix interfaces.SciTopics. Retrieved August 18, 2010, from http://www.scitopics.com/Proteins_motifs_and_protein_assemblies_role_of_helix_helix_interfaces.html

     N. Kurochkina. Helix-helix interfaces and their impact on protein motifs and assemblies. J. Theoretical Biology (2010) 264, 585-92.

     N. Kurochkina,T. Yardeni, and M. Huizing." Molecular modeling of the bifunctional enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase and predictions of structural effects of mutations associated with HIBM and sialuria. Glycobiology 20, 322.

     N. Kurochkina. Specific sequence combinations at parallel and antiparallel helix-helix interfaces. J. Theoretical Biology (2008) 255, 188-198.

     N. Kurochkina. Amino acid composition of parallel helix-helix interfaces. J. Theoretical Biology (2007) 247, 110-121.

     S. Yakovlev, E. Makogonenko, N. Kurochkina, W. Nieuwenhuizen, K. Ingham, L. Medved. Conversion of fibrinogen to fibrin: mechanism of exposure for tPA-plasminogen binding site. Biochemistry, (2000) 39, 15730.

     N.Kurochkina, G. Privalov. Heterogeneity of packing: Structural Approach. Protein Science (1998) 7:897-906 .

     U. Brinkmann, A. Di Carlo, G. Vasmatzis, N. Kurochkina, R. Beers, B. Lee, I. Pastan. Stabilization of a recombinant Fv Fragment by base loop interconnection and VH-VL permutation. J. Mol. Biol. (1997) v. 268, 107-117.

     B. Lee, N. Kurochkina, H.S. Kang. Protein folding by a biased Monte Carlo procedure in the dihedral angle space. Faseb. J. (1996) v.10 (1), 119-125.

     N. Kurochkina, B. Lee. Hydrophobic potential based on pair-wise surfacearea sum. Protein Engineering (1995), v.8, no.5, 437-442.

     N. Kurochkina, Kang, H. B. Lee. Experiences with dihedral angle space Monte Carlo search for small protein structures. in: Statistical mechanics, protein structure and protein-substrate interactions. ed/S. Doniach. Plenum Press, 1994.

     H. S. Kang, N. A. Kurochkina and B. Lee. Estimation and Use of Protein Backbone Angle Probabilities. J. Mol. Biol. (1993) 229, 448-460.

     V. I. Lim, C. Venclovas, N. A. Kurochkina. The path of a protein chain can be approximated by the conformation dictated by interpeptide ionic bridges. FEBS Letters (1992) v.302, 57-60.

     N. A. Kurochkina, V. S. Lamsin, A. P. Savitsky, I. A. Shumilin and V. O. Popov. Mapping of the immunodominant regions of the NAD-dependent formate

dehydrogenase. FEBS Letters (1990) v.260, pp.297-300.

     A. V. Bogdanova, T. V. Cherednikova, T. A. Egorov, E. G. Harutyunyan, Yu. N. Chirgadze, N. A. Kurochkina, S. V. Niconov. Molecular Cartography of Proteins: Surface Relief Analysis of Calf Eye Lens Protein Gamma-crystallin. Protein Engineering (1989) 3, pp.105-110.

     N. A. Nevskaya, N. A. Kurochkina, Yu. N. Chirgadze. The building of the three-dimensional protein structure in electron density maps using computer graphics. Crystallographia (1986) 31, pp. 303-311 (in Russian).

 

CURRENT RESEARCH INTERESTS

 

Structural determinants of cellular signal transduction
Protein Structure

 

 

 

 

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