Macromolecular Modeling Blog ™

In this Bi-Weekly Digest, several folding theory papers and a first look at a large ribonucleoprotein particle which may play a role in pathogen clearance. 

Science:

An intriguing but poorly understood structure, broadly distributed in eukaryotic cells, is a large ribonucleo-protein particle termed a vault–so named because electron microscopy revealed a complex morphology resembling the multiple arches of cathedral vaults. Now Tanaka et al. report the structure of the rat liver vault that shows how the cagelike structure is assembled from 78 subunits with 39-fold dihedral symmetry. One domain has structural similarity to a lipid-raft binding domain, consistent with a previous finding that vaults are recruited to lipid rafts where they may play a role in pathogen clearance.

Byte Size Biology covers this paper in an interesting and highly visual post.

PNAS:

• The transition state for integral membrane protein folding. Paul Curnow and Paula J. Booth
• Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics. Samuel S. Cho, Yaakov Levy, and Peter G. Wolynes
• Identification of direct residue contacts in protein-protein interaction by message passing. Martin Weigt, Robert A. White, Hendrik Szurmant, James A. Hoch, and Terence Hwa
• Folding energy landscape and network dynamics of small globular proteins. Naoto Hori, George Chikenji, R. Stephen Berry, and Shoji Takada.
• Dynamics of one-state downhill protein folding. Peng Li, Fabiana Y. Oliva, Athi N. Naganathan, and Victor Muñoz

Biophysical Journal:

• Application of Elastic Network Models to Proteins in the Crystalline State. Demian Riccardi, Qiang Cui, George N. Phillips
• Role of metal ions in substrate recognition and stability of Concanavalin A: Amolecular dynamics study. Kaushik S, Mohanty D, Surolia A.

Structure:

• Symmetrical Modularity of the COP9 Signalosome Complex Suggests its Multifunctionality. Sharon M, Mao H, Boeri Erba E, Stephens E, Zheng N, Robinson CV.

JMB:

• Collective motions in glucosamine-6-phosphate synthase: influence of ligand binding and role in ammonia channelling and opening of the fructose-6-phosphate binding site. Floquet N, Durand P, Maigret B, Badet B, Badet-Denisot MA, Perahia D.
• In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. Lapelosa M, Gallicchio E, Arnold GF, Arnold E, Levy RM.
• A periodic table of coiled-coil protein structures. Moutevelis E, Woolfson DN.
• Binding hot spot in the weak protein complex of physiological redox partners yeast cytochrome C and cytochrome C peroxidase. Volkov AN, Bashir Q, Worrall JA, Ubbink M.
• OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries. Wu Y, Dousis AD, Chen M, Li J, Ma J.

Proteins:

• Accurate domain identification with structure-anchored hidden Markov models, saHMMs. Jeanette E. Tångrot, Bo Kågström, Uwe H. Sauer
• Merging chemical and biological space: Structural mapping of enzyme binding pocket space. Nils Weskamp, Eyke Hüllermeier, Gerhard Klebe.
• Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. George Khelashvili, Alan Grossfield, Scott E. Feller, Michael C. Pitman, Harel Weinstein
• Refining near-native protein-protein docking decoys by local resampling and energy minimization. Shide Liang, Guangce Wang, Yaoqi Zhou
• Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state. Thomas Splettstoesser, Frank Noé, Toshiro Oda, Jeremy C. Smith
• Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field. Patrick M. Buck, Christopher Bystroff
• A method for the analysis of domain movements in large biomolecular complexes. Guru Prasad Poornam, Atsushi Matsumoto, Hisashi Ishida, Steven Hayward

Journal of computational biology:

• Extended HP Model for Protein Structure Prediction. Tamjidul Hoque, Madhu Chetty, Abdul Sattar.

Current Opinions in Structural Biology:

• Function and structure of inherently disordered proteins. A Keith Dunker, Israel Silman, Vladimir N Uversky and Joel L Sussman.
• Molecular motors of the bacterial flagella. Tohru Minamino, Katsumi Imada and Keiichi Namba
• Structural insights into ABC transporter mechanism. Michael L Oldham, Amy L Davidson

Current Biology:

• Protein Complexes: The Evolution of Symmetry. K.W. Plaxco and M. Gross