Macromolecular Modeling Blog ™

In this Bi-weekly digest, a structural insight into the inhibition mechanism of calpastatins, analysis of core hydrophobic amino acids interactions and more relevant titles form current issues of molecular and computational biology literature. If you want to initiate in a public discussion on one of these, let us know in the comments.

Nature:

• Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains. Moldoveanu T, Gehring K, Green DR.

PNAS:

• Molecular structural basis for polymorphism in Alzheimer’s ?-amyloid fibrils. Anant K. Paravastu, Richard D. Leapman, Wai-Ming Yau, and Robert Tycko.
• High tolerance for ionizable residues in the hydrophobic interior of proteins. Daniel G. Isom, Brian R. Cannon, Carlos A. Castañeda, Aaron Robinson, and Bertrand García-Moreno E.
• Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability. S. Vaitheeswaran and D. Thirumalai.

JACS:

• Ab Initio Modeling of Protein/Biomaterial Interactions: Glycine Adsorption at Hydroxyapatite Surfaces. Albert Rimola, Marta Corno, Claudio Marcelo Zicovich-Wilson and Piero Ugliengo.
• Engineering Complex Riboswitch Regulation by Dual Genetic Selection. Vandana Sharma, Yoko Nomura and Yohei Yokobayashi

Bioinformatics:

• A novel method for comparing topological models of protein structures enhanced with ligand information. Mallika Veeramalai and David Gilbert
• Searching protein structure databases with DaliLite v.3. Holm, S. Kääriäinen, P. Rosenström, and A. Schenkel

Proteins:

• Local descriptors of protein structure: A systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. Torgeir R. Hvidsten, Andriy Kryshtafovych, Krzysztof Fidelis

Journal of Computational Biology:

• Pseudoknot RNA Structures with Arc-Length ? 4. Hillary S.W. Han, Christian M. Reidys.

• Dynameomics: Large-scale assessment of native protein flexibility. Noah C. Benson and Valerie Daggett

JMB: 

• The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design. Olsson TS, Williams MA, Pitt WR, Ladbury JE.

Structure:

• Protein metamorphosis: the two-state behavior of mad2. Luo X, Yu H.

Biophysical Journal:

• A simplified model of local structure in aqueous proline amino acid revealed by first principles molecular dynamics simulations. Troitzsch RZ, Tulip PR, Crain J, Martyna GJ.
• Generalized pattern search algorithm for Peptide structure prediction. Nicosia G, Stracquadanio G.

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