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Nguyen PH, Keller JE, Novitsky YW, Heniford BT, Kercher KW. Laparoscopic approach to adrenalectomy: review of perioperative outcomes in a single center. Am Surg 2011; 77:592-596. [PMID: 21679593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Laparoscopic expertise increases the volume of adrenalectomies at referral centers. We report our 10-year experience with laparoscopic adrenalectomy. All laparoscopic adrenalectomies at a single institution were prospectively recorded in a surgical outcomes database. Patient demographics, operative/perioperative outcomes, and adrenal pathology were reviewed retrospectively. From March 1999 through July 2009, 154 laparoscopic adrenalectomies were performed in 150 patients. Average patient age was 49.9 years (range 15-82); mean body mass index was 31.1 kg/m(2) (range 17-56). Pathologic diagnoses included hyperaldosteronism (n = 69), nonfunctional adenoma (n = 28), pheochromocytoma (n = 23), hypercortisolism (n = 14), malignancy (primary n = 3, metastasis n = 9), and cyst (n = 4). Seventy-three per cent (n = 110) occurred on the left, 23 per cent (n = 35) on the right, 2.6 per cent (n = 4) bilateral, and 0.6 per cent (n = 1) as extra-adrenal. The average tumor measured 3.6 cm (range 0.4-12). The average operative time was 156 minutes (range 62-409), the mean estimated blood loss was 60 mL (range 10-400), and mean American Society of Anesthesiologists score was 2.6 (range 1-4). Three operations (0.2%) were converted to open. Three patients (0.2%) experienced perioperative complications (respiratory failure, urinary tract infection, line sepsis, and readmission within 30 days). The average length of stay was 3.4 days (range 1-44) and mean follow-up was 96.9 days (5-2567). No wound-related complications or deaths occurred. Pathologic diagnosis was not associated with a particular side or development of a complication (P > 0.5). Patients with pheochromocytomas had the longest operative times, highest estimated blood loss, and highest American Society of Anesthesiologists scores (218.2 minutes, 128 mL, 3.0; P < 0.004). Laparoscopic adrenalectomy is safe and effective. Removal of pheochromocytomas is more challenging and may be more appropriate for referral to a specialized center for optimal outcomes.
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Nguyen PH, Keller JE, Novitsky YW, Heniford BT, Kercher KW. Laparoscopic Approach to Adrenalectomy: Review of Perioperative Outcomes in a Single Center. Am Surg 2011. [DOI: 10.1177/000313481107700519] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Laparoscopic expertise increases the volume of adrenalectomies at referral centers. We report our 10-year experience with laparoscopic adrenalectomy. All laparoscopic adrenalectomies at a single institution were prospectively recorded in a surgical outcomes database. Patient demographics, operative/perioperative outcomes, and adrenal pathology were reviewed retrospectively. From March 1999 through July 2009, 154 laparoscopic adrenalectomies were performed in 150 patients. Average patient age was 49.9 years (range 15-82); mean body mass index was 31.1 kg/m2 (range 17-56). Pathologic diagnoses included hyperaldosteronism (n = 69), nonfunctional adenoma (n = 28), pheochromocytoma (n = 23), hypercortisolism (n = 14), malignancy (primary n = 3, metastasis n = 9), and cyst (n = 4). Seventy-three per cent (n = 110) occurred on the left, 23 per cent (n = 35) on the right, 2.6 per cent (n = 4) bilateral, and 0.6 per cent (n = 1) as extra-adrenal. The average tumor measured 3.6 cm (range 0.4-12). The average operative time was 156 minutes (range 62-409), the mean estimated blood loss was 60 mL (range 10–100), and mean American Society of Anesthesiologists score was 2.6 (range 1-4). Three operations (0.2%) were converted to open. Three patients (0.2%) experienced perioperative complications (respiratory failure, urinary tract infection, line sepsis, and readmission within 30 days). The average length of stay was 3.4 days (range 1–14) and mean follow-up was 96.9 days (5-2567). No wound-related complications or deaths occurred. Pathologic diagnosis was not associated with a particular side or development of a complication ( P > 0.5). Patients with pheochromocytomas had the longest operative times, highest estimated blood loss, and highest American Society of Anesthesiologists scores (218.2 minutes, 128 mL, 3.0; P < 0.004). Laparoscopic adrenalectomy is safe and effective. Removal of pheochromocytomas is more challenging and may be more appropriate for referral to a specialized center for optimal outcomes.
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Hoang LN, Hajeebhoy N, Nguyen PH, Lapping K, Frongillo EA, Menon P. Using content analysis to assess quality of provincial nutrition plans in Vietnam. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.108.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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154
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Kobus M, Nguyen PH, Stock G. Coherent vibrational energy transfer along a peptide helix. J Chem Phys 2011; 134:124518. [DOI: 10.1063/1.3574395] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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155
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Nguyen PH, Li MS, Derreumaux P. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer. Phys Chem Chem Phys 2011; 13:9778-88. [DOI: 10.1039/c1cp20323a] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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156
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Kobus M, Nguyen PH, Stock G. Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study. J Chem Phys 2010; 133:034512. [DOI: 10.1063/1.3462961] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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157
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Sing RF, Nguyen PH, Christmas AB, Jacobs DG, Heniford BT. Vena Cava Filter Insertion and the General Surgery Armamentarium: A 13-Year Experience. Am Surg 2010. [DOI: 10.1177/000313481007600725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The prevention of pulmonary emboli has a long surgical history. Through the development of percutaneous technologies, vena cava filters (VCFs) are now commonly inserted by interventional radiologists. This study reviews our experience with VCFs inserted by general surgeons. We retrospectively reviewed data from our VCF performance improvement database, which is a prospective collection of the VCF experience of the Department of General Surgery from February 1996 to May 2009. Demographics, procedural information, and complications were recorded. Eight hundred fifty-five VCFs were inserted in 853 patients. The mean age was 42.0 years (range, 14 to 90 years). One hundred ninety-seven VCFs were placed in the operating room, and 658 were placed in the intensive care unit. Twelve VCFs were intentionally inserted in a suprarenal position, and four were placed in the superior vena cava. Two patients received both superior vena cava and inferior vena cava filters. Complications included deep vein thrombosis at the insertion site (n = 16), vena cava thrombosis (n = 9), post-VCF pulmonary embolism (n = 2), and a ventricle perforation requiring operative repair (n = 1). No deaths were attributed to the presence of a VCF. Overall insertion success was 99.8 per cent. In two patients, an inferior VCF could not be placed as a result of inferior vena cava occlusion with no safe “landing zone” for deployment. The placement of VCFs is a vital skill in the general surgery armamentarium. Our experience demonstrates that general surgeons can safely insert VCFs with minimal perioperative complications.
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Sing RF, Nguyen PH, Christmas AB, Jacobs DG, Heniford BT. Vena cava filter insertion and the general surgery armamentarium: a 13-year experience. Am Surg 2010; 76:713-717. [PMID: 20698376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The prevention of pulmonary emboli has a long surgical history. Through the development of percutaneous technologies, vena cava filters (VCFs) are now commonly inserted by interventional radiologists. This study reviews our experience with VCFs inserted by general surgeons. We retrospectively reviewed data from our VCF performance improvement database, which is a prospective collection of the VCF experience of the Department of General Surgery from February 1996 to May 2009. Demographics, procedural information, and complications were recorded. Eight hundred fifty-five VCFs were inserted in 853 patients. The mean age was 42.0 years (range, 14 to 90 years). One hundred ninety-seven VCFs were placed in the operating room, and 658 were placed in the intensive care unit. Twelve VCFs were intentionally inserted in a suprarenal position, and four were placed in the superior vena cava. Two patients received both superior vena cava and inferior vena cava filters. Complications included deep vein thrombosis at the insertion site (n=16), vena cava thrombosis (n=9), post-VCF pulmonary embolism (n=2), and a ventricle perforation requiring operative repair (n=1). No deaths were attributed to the presence of a VCF. Overall insertion success was 99.8 per cent. In two patients, an inferior VCF could not be placed as a result of inferior vena cava occlusion with no safe "landing zone" for deployment. The placement of VCFs is a vital skill in the general surgery armamentarium. Our experience demonstrates that general surgeons can safely insert VCFs with minimal perioperative complications.
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159
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Nguyen PH. Replica exchange simulation method using temperature and solvent viscosity. J Chem Phys 2010; 132:144109. [DOI: 10.1063/1.3369626] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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160
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Riccardi L, Nguyen PH, Stock G. Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis. J Phys Chem B 2010; 113:16660-8. [PMID: 20028141 DOI: 10.1021/jp9076036] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
To systematically construct a low-dimensional free-energy landscape of RNA systems from a classical molecular dynamics simulation, various versions of the principal component analysis (PCA) are compared: the cPCA using the Cartesian coordinates of all atoms, the dPCA using the sine/cosine-transformed six backbone dihedral angles as well as the glycosidic torsional angle chi and the pseudorotational angle P, the aPCA which ignores the circularity of the 6 + 2 dihedral angles of the RNA, and the dPCA(etatheta), which approximates the 6 backbone dihedral angles by 2 pseudotorsional angles eta and theta. As representative examples, a 10-nucleotide UUCG hairpin and the 36-nucleotide segment SL1 of the Psi site of HIV-1 are studied by classical molecular dynamics simulation, using the Amber all-atom force field and explicit solvent. It is shown that the conformational heterogeneity of the RNA hairpins can only be resolved by an angular PCA such as the dPCA but not by the cPCA using Cartesian coordinates. Apart from possible artifacts due to the coupling of overall and internal motion, this is because the details of hydrogen bonding and stacking interactions but also of global structural rearrangements of the RNA are better discriminated by dihedral angles. In line with recent experiments, it is found that the free energy landscape of RNA hairpins is quite rugged and contains various metastable conformational states which may serve as an intermediate for unfolding.
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161
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Nguyen PH, Park SM, Stock G. Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix. J Chem Phys 2010; 132:025102. [DOI: 10.1063/1.3284742] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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162
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Park SM, Nguyen PH, Stock G. Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J Chem Phys 2009; 131:184503. [DOI: 10.1063/1.3259971] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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163
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Nguyen PH, Grajeda R, Melgar P, Marcinkevage J, DiGirolamo AM, Flores R, Martorell R. Micronutrient supplementation may reduce symptoms of depression in Guatemalan women. ARCHIVOS LATINOAMERICANOS DE NUTRICION 2009; 59:278-286. [PMID: 19886513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Evidence for the impact of micronutrient supplementation trials on depression in women from developing countries is limited. This study examines this association and compares the impact of weekly versus daily combinations of micronutrient supplements on symptoms of depression. A randomized, positive-controlled trial was conducted in Guatemala. A total of 459 women were assigned randomly to 4 groups to receive weekly (5,000 or 2,800 microg) or daily (400 or 200 microg) folic acid (FA) plus iron, zinc and vitamin B-12 for 12 weeks. Depression was measured using the Center for Epidemiologic Studies-Depression 20-item Scale (CES-D). A score = 16 was used as an indication of depression. The association between micronutrient status and depression was assessed using baseline data. Generalized linear regression models were used to assess treatment effects. The baseline mean CES-D score was 17.1 +/- 8.5 and the prevalence of depression was 49.3%. Women in the lowest tertile of red blood cell folate (RBC) were 1.7 times more likely to be depressed than those in the highest tertile (OR=1.71; 95% CI: 0.91, 3.18). There were no associations between depression and serum folate, homocysteine, vitamin B-12, hemoglobin, ferritin or zinc (p > 0.05). Mean depression scores decreased by 2.3 points post-intervention and depression decreased to 37.7%, with no differences in degree of improvement by group (p = 0.64). Low RBC folate was associated with elevated symptoms of depression at baseline. Supplementation with FA-containing micronutrients may be equally efficacious in improving symptoms of depression when provided daily or weekly. Our findings that poor folate status may increase depression needs to be further investigated.
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164
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Nguyen PH, Derreumaux P, Stock G. Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study. J Phys Chem B 2009; 113:9340-7. [DOI: 10.1021/jp902013s] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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165
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Rivera V, Nguyen PH, Sit A. Change in quantitative human chorionic gonadotropin after manual vacuum aspiration in women with pregnancy of unknown location. Am J Obstet Gynecol 2009; 200:e56-9. [PMID: 19168172 DOI: 10.1016/j.ajog.2008.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 10/01/2008] [Accepted: 10/07/2008] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To determine whether the change in human chorionic gonadotropin after manual vacuum aspiration is predictive of an early abnormal intrauterine pregnancy in women with pregnancy of unknown location. STUDY DESIGN This is a prospective cohort study of 23 clinically stable patients with an early abnormal pregnancy who had abnormally rising human chorionic gonadotropins and absence of sonographic evidence of an intrauterine pregnancy or ectopic pregnancy. The change in human chorionic gonadotropin within 24 hours after manual vacuum aspiration was compared with the pathologic diagnosis and the ultimate clinical diagnosis. RESULTS Ten patients had > or = 50% decrease (mean, 74%; range, 58-80%) in human chorionic gonadotropin after manual vacuum aspiration with confirmed chorionic villi on pathology results. Two patients had a > 50% drop in human chorionic gonadotropin but absence of chorionic villi, clinically consistent with complete spontaneous abortion. The remaining 10 patients who had either rising or < 50% decrease in human chorionic gonadotropin post manual vacuum aspiration all had no chorionic villi on pathology results. The sensitivity, specificity, positive predictive value, and negative predictive value of a > or = 50% decrease in human chorionic gonadotropin after manual vacuum aspiration in predicting an abnormal intrauterine pregnancy were 92% (95% confidence interval [CI], 0.62-0.99), 100% (95% CI, 0.62-1.0), 100% (95% CI, 0.70-1.0), and 90% (95% CI, 0.54-0.99), respectively. CONCLUSION A > or = 50% decrease in human chorionic gonadotropin within 24 hours after manual vacuum aspiration is predictive of an abnormal intrauterine pregnancy, thereby excluding an ectopic pregnancy and expediting the management of women with pregnancy of unknown location.
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166
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Backus EHG, Nguyen PH, Botan V, Moretto A, Crisma M, Toniolo C, Zerbe O, Stock G, Hamm P. Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties. J Phys Chem B 2008; 112:15487-92. [DOI: 10.1021/jp806403p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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167
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Altis A, Otten M, Nguyen PH, Hegger R, Stock G. Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis. J Chem Phys 2008; 128:245102. [PMID: 18601386 DOI: 10.1063/1.2945165] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A systematic approach to construct a low-dimensional free energy landscape from a classical molecular dynamics (MD) simulation is presented. The approach is based on the recently proposed dihedral angle principal component analysis (dPCA), which avoids artifacts due to the mixing of internal and overall motions in Cartesian coordinates and circumvents problems associated with the circularity of angular variables. Requiring that the energy landscape reproduces the correct number, energy, and location of the system's metastable states and barriers, the dimensionality of the free energy landscape (i.e., the number of essential components) is obtained. This dimensionality can be determined from the distribution and autocorrelation of the principal components. By performing an 800 ns MD simulation of the folding of hepta-alanine in explicit water and using geometric and kinetic clustering techniques, it is shown that a five-dimensional dPCA energy landscape is a suitable and accurate representation of the full-dimensional landscape. In the second step, the dPCA energy landscape can be employed (e.g., in a Langevin simulation) to facilitate a detailed investigation of biomolecular dynamics in low dimensions. Finally, several ways to visualize the multidimensional energy landscape are discussed.
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168
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Backus EHG, Nguyen PH, Botan V, Pfister R, Moretto A, Crisma M, Toniolo C, Stock G, Hamm P. Energy Transport in Peptide Helices: A Comparison between High- and Low-Energy Excitations. J Phys Chem B 2008; 112:9091-9. [DOI: 10.1021/jp711046e] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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169
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Altis A, Nguyen PH, Hegger R, Stock G. Dihedral angle principal component analysis of molecular dynamics simulations. J Chem Phys 2007; 126:244111. [PMID: 17614541 DOI: 10.1063/1.2746330] [Citation(s) in RCA: 227] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {phi(n)} to the metric coordinate space {x(n)=cos phi(n),y(n)=sin phi(n)} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300 ns molecular dynamics simulation, a critical comparison of the various methods is given.
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170
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Botan V, Backus EHG, Pfister R, Moretto A, Crisma M, Toniolo C, Nguyen PH, Stock G, Hamm P. Energy transport in peptide helices. Proc Natl Acad Sci U S A 2007; 104:12749-54. [PMID: 17646650 PMCID: PMC1937538 DOI: 10.1073/pnas.0701762104] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Indexed: 11/18/2022] Open
Abstract
We investigate energy transport through an alpha-aminoisobutyric acid-based 3(10)-helix dissolved in chloroform in a combined experimental-theoretical approach. Vibrational energy is locally deposited at the N terminus of the helix by ultrafast internal conversion of a covalently attached, electronically excited, azobenzene moiety. Heat flow through the helix is detected with subpicosecond time resolution by employing vibrational probes as local thermo meters at various distances from the heat source. The experiment is supplemented by detailed nonequilibrium molecular dynamics (MD) simulations of the process, revealing good qualitative agreement with experiment: Both theory and experiment exhibit an almost instantaneous temperature jump of the reporter units next to the heater which is attributed to the direct impact of the isomerizing azobenzene moiety. After this impact event, helix and azobenzene moiety appear to be thermally decoupled. The energy deposited in the helix thermalizes on a subpicosecond timescale and propagates along the helix in a diffusive-like process, accompanied by a significant loss into the solvent. However, in terms of quantitative numbers, theory and experiment differ. In particular, the MD simulation seems to overestimate the heat diffusion constant (2 A(2) ps(-1) from the experiment) by a factor of five.
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171
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Dager WE, Dougherty JA, Nguyen PH, Militello MA, Smythe MA. Heparin-Induced Thrombocytopenia: Treatment Options and Special Considerations. Pharmacotherapy 2007; 27:564-87. [PMID: 17381384 DOI: 10.1592/phco.27.4.564] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Heparin-induced thrombocytopenia (HIT) is an immune-mediated adverse effect that typically manifests several days after the start of heparin therapy, although both rapid- and delayed-onset HIT have been described. Its most serious complication is thrombosis. Although not all patients develop thrombosis, it can be life threatening. The risk of developing HIT is related to many factors, including the type of heparin product administered, route of administration, duration of therapy, patient population, and previous exposure to heparin. The diagnosis of HIT is typically based on clinical presentation, exposure to heparin, and presence of thrombocytopenia with or without thrombosis. Antigen and activation laboratory assays are available to support the diagnosis of HIT. However, because of the limited sensitivity and specificity of these assays, bedside probability scales for HIT were developed. When HIT is suspected, prompt cessation of all heparin therapy is necessary, along with initiation of alternative anticoagulant therapy. Two direct thrombin inhibitors--argatroban and lepirudin--are approved for the management of HIT in the United States, and bivalirudin is approved for use in patients with HIT who are undergoing percutaneous coronary intervention. Other agents, although not approved to manage HIT, have also been used; however, their role in therapy requires further evaluation. A comprehensive HIT management strategy involves the evaluation of numerous factors. Many patients, including those undergoing coronary artery bypass surgery, those with acute coronary syndromes, those with hepatic or renal insufficiency, and children, require special attention. Clinicians must become familiar with the available information on this serious adverse effect and its treatment so that optimum patient management strategies may be formulated.
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172
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Graf J, Nguyen PH, Stock G, Schwalbe H. Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study. J Am Chem Soc 2007; 129:1179-89. [PMID: 17263399 DOI: 10.1021/ja0660406] [Citation(s) in RCA: 259] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The phi,psi backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of <5 %. Trialanine samples mainly ( approximately 90%) a poly-l-proline II helix-like structure, some ( approximately 10%) beta extended structure, but no alphaR helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala(3) to Ala(7)). Trivaline samples all three major conformations significantly. Triglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala(3)-Ala(7), major differences are found for the 19mer, which significantly (30-40%) samples alphaR helical stuctures.
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173
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Nguyen PH. Conformational states and folding pathways of peptides revealed by principal-independent component analyses. Proteins 2007; 67:579-92. [PMID: 17348012 DOI: 10.1002/prot.21317] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Principal component analysis is a powerful method for projecting multidimensional conformational space of peptides or proteins onto lower dimensional subspaces in which the main conformations are present, making it easier to reveal the structures of molecules from e.g. molecular dynamics simulation trajectories. However, the identification of all conformational states is still difficult if the subspaces consist of more than two dimensions. This is mainly due to the fact that the principal components are not independent with each other, and states in the subspaces cannot be visualized. In this work, we propose a simple and fast scheme that allows one to obtain all conformational states in the subspaces. The basic idea is that instead of directly identifying the states in the subspace spanned by principal components, we first transform this subspace into another subspace formed by components that are independent of one other. These independent components are obtained from the principal components by employing the independent component analysis method. Because of independence between components, all states in this new subspace are defined as all possible combinations of the states obtained from each single independent component. This makes the conformational analysis much simpler. We test the performance of the method by analyzing the conformations of the glycine tripeptide and the alanine hexapeptide. The analyses show that our method is simple and quickly reveal all conformational states in the subspaces. The folding pathways between the identified states of the alanine hexapeptide are analyzed and discussed in some detail.
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174
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Gorbunov RD, Nguyen PH, Kobus M, Stock G. Quantum-classical description of the amide I vibrational spectrum of trialanine. J Chem Phys 2007; 126:054509. [PMID: 17302487 DOI: 10.1063/1.2431803] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A quantum-classical description of the amide I vibrational spectrum of trialanine cation in D2O is given that combines (i) a classical molecular dynamics simulation of the conformational distribution of the system, (ii) comprehensive density functional theory calculations of the conformation-dependent and solvent-induced frequency fluctuations, and (iii) a semiclassical description of the vibrational line shapes which includes nonadiabatic transitions between vibrational eigenstates. Various assumptions that are usually employed in the calculation of condensed-phase vibrational spectra are tested, including the adiabatic, the Franck-Condon, and the second-order cumulant approximations, respectively. All three parts of the theoretical formulation are shown to have a significant impact on the simulated spectrum, suggesting that the interpretation of peptide amide I spectra may require substantial theoretical support.
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175
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Hegger R, Altis A, Nguyen PH, Stock G. How complex is the dynamics of Peptide folding? PHYSICAL REVIEW LETTERS 2007; 98:028102. [PMID: 17358652 DOI: 10.1103/physrevlett.98.028102] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Indexed: 05/14/2023]
Abstract
Classical molecular dynamics simulations of the folding of alanine peptides in aqueous solution are analyzed by constructing a deterministic model of the dynamics, using methods from nonlinear time series analysis. While the dimension of the free energy landscape increases with system size, a Lyapunov analysis shows that the effective dimension of the dynamic system is rather small and even decreases with chain length. The observed reduction of phase space is a nonlinear cooperative effect that is caused by intramolecular hydrogen bonds that stabilize the secondary structure of the peptides.
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